https://www.slicer.org/w/api.php?action=feedcontributions&user=Frederic&feedformat=atomSlicer Wiki - User contributions [en]2024-03-29T00:22:23ZUser contributionsMediaWiki 1.33.0https://www.slicer.org/w/index.php?title=Documentation/4.11/Modules/GeodesicSlicer&diff=63899Documentation/4.11/Modules/GeodesicSlicer2021-12-16T10:23:58Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}<br />
</noinclude><br />
<br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
<br />
:'''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
:'''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
:'''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
*Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
*Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
*Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
*Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/ ISTS].<br />
*Dr. Csaba Pinter, MSc, Queen's University.<br />
*Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2020a">Briend F. et al., A new toolbox to compare NIBS localization method: Application for auditory hallucinations in schizophrenia. Schizophrenia Research, https://doi.org/10.1016/j.schres.2020.09.001</ref> and <ref name="Briend 2020b">Briend F. et al., GeodesicSlicer: a Slicer Toolbox for Targeting Brain Stimulation. Neuroinformatics. https://doi.org/10.1007/s12021-020-09457-9</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref><br />
<br />
<!-- ---------------------------- --><br />
#First, open 3D Slicer<br />
#Open the Slicer Extensions from the icon on the menu bar<br />
#Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
#Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)<br />
<br />
<!-- ---------------------------- --><br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- -->====Create a mesh====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
#Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
#Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
#Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
====Parameters to find the shortest path====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
#Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).<br />
#Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#*Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#*Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#**Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
<br />
#4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#*1/ The nasion<br />
#*2/ The inion<br />
#*3/ The pre auricular to the left ear<br />
#*4/ The pre auricular to the right ear<br />
#Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#*The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
<br />
#Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
#Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#*Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#*Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#*Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
#M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
#Set the stimulation intensity of the resting motor threshold.<br />
#Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#*Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1.<br />
#*1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT]<br />
#*2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)]<br />
<br />
<!-- ---------------------------- --><br />
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
<br /><references /></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.11/Modules/GeodesicSlicer&diff=63898Documentation/4.11/Modules/GeodesicSlicer2021-12-16T10:22:12Z<p>Frederic: Created page with "<noinclude>{{documentation/versioncheck}}</noinclude> <!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- -----------------..."</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/ ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2020a">Briend F. et al., A new toolbox to compare NIBS localization method: Application for auditory hallucinations in schizophrenia. Schizophrenia Research, https://doi.org/10.1016/j.schres.2020.09.001</ref> and <ref name="Briend 2020b">Briend F. et al., GeodesicSlicer: a Slicer Toolbox for Targeting Brain Stimulation. Neuroinformatics. https://doi.org/10.1007/s12021-020-09457-9</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.10/Modules/GeodesicSlicer&diff=63450Documentation/4.10/Modules/GeodesicSlicer2020-10-16T09:31:15Z<p>Frederic: add DOI</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/ ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2020a">Briend F. et al., A new toolbox to compare NIBS localization method: Application for auditory hallucinations in schizophrenia. Schizophrenia Research, https://doi.org/10.1016/j.schres.2020.09.001</ref> and <ref name="Briend 2020b">Briend F. et al., GeodesicSlicer: a Slicer Toolbox for Targeting Brain Stimulation. Neuroinformatics. https://doi.org/10.1007/s12021-020-09457-9</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/GeodesicSlicer&diff=63449Documentation/Nightly/Modules/GeodesicSlicer2020-10-16T09:30:16Z<p>Frederic: add DOI</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}<br />
</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
*Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
*Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
*Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
*Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
*Dr. Csaba Pinter, MSc, Queen's University.<br />
*Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2020a">Briend F. et al., A new toolbox to compare NIBS localization method: Application for auditory hallucinations in schizophrenia. Schizophrenia Research, https://doi.org/10.1016/j.schres.2020.09.001</ref> and <ref name="Briend 2020b">Briend F. et al., GeodesicSlicer: a Slicer Toolbox for Targeting Brain Stimulation. Neuroinformatics. https://doi.org/10.1007/s12021-020-09457-9</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation}}<br />
<br />
#First, open 3D Slicer<br />
#Open the Slicer Extensions from the icon on the menu bar<br />
#Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
#Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
====Create a mesh====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
#Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
#Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
#Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
====Parameters to find the shortest path====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
#Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).<br />
#Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#*Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#*Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#**Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
<br />
#4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#*1/ The nasion<br />
#*2/ The inion<br />
#*3/ The pre auricular to the left ear<br />
#*4/ The pre auricular to the right ear<br />
#Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#*The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
<br />
#Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
#Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#*Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#*Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#*Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
#M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
#Set the stimulation intensity of the resting motor threshold.<br />
#Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#*Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1.<br />
#*1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT]<br />
#*2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --><br />
<references /></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/GeodesicSlicer&diff=63108Documentation/Nightly/Modules/GeodesicSlicer2020-03-12T09:57:51Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}<br />
</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
*Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
*Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
*Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
*Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
*Dr. Csaba Pinter, MSc, Queen's University.<br />
*Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2019a">Briend F. et al., A new toolbox to compare NIBS localization method: Application for auditory hallucinations in schizophrenia. Schizophrenia Research, submitted</ref> and <ref name="Briend 2019b">Briend F. et al., GeodesicSlicer: a Slicer Toolbox for Targeting Brain Stimulation. Neuroinformatics. https://doi.org/10.1007/s12021-020-09457-9</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation}}<br />
<br />
#First, open 3D Slicer<br />
#Open the Slicer Extensions from the icon on the menu bar<br />
#Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
#Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
====Create a mesh====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
#Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
#Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
#Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
====Parameters to find the shortest path====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
#Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).<br />
#Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#*Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#*Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#**Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
<br />
#4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#*1/ The nasion<br />
#*2/ The inion<br />
#*3/ The pre auricular to the left ear<br />
#*4/ The pre auricular to the right ear<br />
#Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#*The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
<br />
#Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
#Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#*Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#*Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#*Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
#M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
#Set the stimulation intensity of the resting motor threshold.<br />
#Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#*Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1.<br />
#*1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT]<br />
#*2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --><br />
<references /></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.10/Modules/GeodesicSlicer&diff=63107Documentation/4.10/Modules/GeodesicSlicer2020-03-12T09:56:25Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/ ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2019a">Briend F. et al., A new toolbox to compare NIBS localization method: Application for auditory hallucinations in schizophrenia. Schizophrenia Research, submitted</ref> and <ref name="Briend 2019b">Briend F. et al., GeodesicSlicer: a Slicer Toolbox for Targeting Brain Stimulation. Neuroinformatics. https://doi.org/10.1007/s12021-020-09457-9</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.10/Modules/GeodesicSlicer&diff=62778Documentation/4.10/Modules/GeodesicSlicer2019-12-20T10:25:10Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/ ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2019a">Briend F. et al., A new toolbox to compare NIBS localization method: Application for auditory hallucinations in schizophrenia. Schizophrenia Research, submitted</ref> and <ref name="Briend 2019b">Briend F. et al., GeodesicSlicer: A Slicer toolbox for targeting brain stimulation. Neuroinformatics, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/GeodesicSlicer&diff=62777Documentation/Nightly/Modules/GeodesicSlicer2019-12-20T10:24:43Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}<br />
</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
*Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
*Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
*Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
*Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
*Dr. Csaba Pinter, MSc, Queen's University.<br />
*Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2019a">Briend F. et al., A new toolbox to compare NIBS localization method: Application for auditory hallucinations in schizophrenia. Schizophrenia Research, submitted</ref> and <ref name="Briend 2019b">Briend F. et al., GeodesicSlicer: A Slicer toolbox for targeting brain stimulation. Neuroinformatics, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation}}<br />
<br />
#First, open 3D Slicer<br />
#Open the Slicer Extensions from the icon on the menu bar<br />
#Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
#Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
====Create a mesh====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
#Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
#Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
#Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
====Parameters to find the shortest path====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
#Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).<br />
#Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#*Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#*Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#**Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
<br />
#4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#*1/ The nasion<br />
#*2/ The inion<br />
#*3/ The pre auricular to the left ear<br />
#*4/ The pre auricular to the right ear<br />
#Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#*The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
<br />
#Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
#Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#*Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#*Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#*Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
#M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
#Set the stimulation intensity of the resting motor threshold.<br />
#Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#*Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1.<br />
#*1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT]<br />
#*2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --><br />
<references /></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.10/Modules/GeodesicSlicer&diff=61457Documentation/4.10/Modules/GeodesicSlicer2019-09-17T17:09:20Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/ ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2019a">Briend F. et al., A new toolbox to compare NIBS localization method: Application for auditory hallucinations in schizophrenia. Acta Psychiatrica Scandinavica, submitted</ref> and <ref name="Briend 2019b">Briend F. et al., GeodesicSlicer: A Slicer toolbox for targeting brain stimulation. Neuroinformatics, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/GeodesicSlicer&diff=61456Documentation/Nightly/Modules/GeodesicSlicer2019-09-17T17:08:37Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2019a">Briend F. et al., A new toolbox to compare NIBS localization method: Application for auditory hallucinations in schizophrenia. Acta Psychiatrica Scandinavica, submitted</ref> and <ref name="Briend 2019b">Briend F. et al., GeodesicSlicer: A Slicer toolbox for targeting brain stimulation. Neuroinformatics, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/GeodesicSlicer&diff=61455Documentation/Nightly/Modules/GeodesicSlicer2019-09-17T17:07:53Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2019">Briend F. et al., A new toolbox to compare NIBS localization method: Application for auditory hallucinations in schizophrenia. Acta Psychiatrica Scandinavica, submitted</ref> and <ref name="Briend 2019">Briend F. et al., GeodesicSlicer: A Slicer toolbox for targeting brain stimulation. Neuroinformatics, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/GeodesicSlicer&diff=61453Documentation/Nightly/Modules/GeodesicSlicer2019-09-17T15:38:57Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2019">Briend F. et al., A new toolbox to compare target localizations for non-invasive brain stimulation: An application of rTMS treatment for auditory hallucinations in schizophrenia. Acta Psychiatrica Scandinavica, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.10/Modules/GeodesicSlicer&diff=61450Documentation/4.10/Modules/GeodesicSlicer2019-09-16T15:49:09Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/ ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2019">Briend F. et al., A new toolbox to compare target localizations for non-invasive brain stimulation: An application of rTMS treatment for auditory hallucinations in schizophrenia. Acta Psychiatrica Scandinavica, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/GeodesicSlicer&diff=61449Documentation/Nightly/Modules/GeodesicSlicer2019-09-16T15:48:42Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2019">Briend F. et al., A new toolbox to compare target localizations for non-invasive brain stimulation: An application of rTMS treatment for auditory hallucinations in schizophrenia. Acta Psychiatrica Scandinavica, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.10/Modules/GeodesicSlicer&diff=61416Documentation/4.10/Modules/GeodesicSlicer2019-09-11T20:55:35Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/ ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2019">Briend F. et al., A new toolbox to compare target localizations for non-invasive brain stimulation: An application of rTMS treatment for auditory hallucinations in schizophrenia. NeuroImage Clinical, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/GeodesicSlicer&diff=61415Documentation/Nightly/Modules/GeodesicSlicer2019-09-11T20:54:56Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2019">Briend F. et al., A new toolbox to compare target localizations for non-invasive brain stimulation: An application of rTMS treatment for auditory hallucinations in schizophrenia. NeuroImage Clinical, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/GeodesicSlicer&diff=61392Documentation/Nightly/Modules/GeodesicSlicer2019-09-04T21:41:37Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2019">Briend F. et al., A new toolbox to compare target localizations for non-invasive brain stimulation: An application of rTMS treatment for auditory hallucinations in schizophrenia. NeuroImage, Special Issue, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/GeodesicSlicer&diff=61391Documentation/Nightly/Modules/GeodesicSlicer2019-09-04T18:44:15Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2019">Briend F. et al., A new toolbox to compare target localizations for non-invasive brain stimulation: An application of rTMS treatment for auditory hallucinations in schizophrenia. NeuroImage, Special Issue, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/nourryan/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.10/Modules/GeodesicSlicer&diff=61390Documentation/4.10/Modules/GeodesicSlicer2019-09-04T18:32:56Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/ ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2019">Briend F. et al., A new toolbox to compare target localizations for non-invasive brain stimulation: An application of rTMS treatment for auditory hallucinations in schizophrenia. NeuroImage, Special Issue, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.10/Modules/GeodesicSlicer&diff=61302Documentation/4.10/Modules/GeodesicSlicer2019-07-18T20:32:01Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/ ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2019">Briend F. et al., A new toolbox to compare target localizations for non-invasive brain stimulation: An application of rTMS treatment for auditory hallucinations in schizophrenia. Schizophrenia Bulletin, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.10/Modules/GeodesicSlicer&diff=61301Documentation/4.10/Modules/GeodesicSlicer2019-07-18T20:30:03Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2019">Briend F. et al., A new toolbox to compare target localizations for non-invasive brain stimulation: An application of rTMS treatment for auditory hallucinations in schizophrenia. Schizophrenia Bulletin, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.10/Modules/GeodesicSlicer&diff=61296Documentation/4.10/Modules/GeodesicSlicer2019-07-15T16:38:16Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2019">Briend F. et al., A new toolbox to compare target localizations for non-invasive brain stimulation: An application of rTMS treatment for auditory hallucinations in schizophrenia. Schizophrenia Bulletin, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.10/Modules/GeodesicSlicer&diff=60724Documentation/4.10/Modules/GeodesicSlicer2019-01-16T20:29:20Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Repetitive transcranial magnetic stimulation (rTMS) treatment for auditory hallucinations: personalized or standardized targets? Brain Stimulation, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/GeodesicSlicer&diff=60723Documentation/Nightly/Modules/GeodesicSlicer2019-01-16T20:28:40Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Repetitive transcranial magnetic stimulation (rTMS) treatment for auditory hallucinations: personalized or standardized targets? Brain Stimulation, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/nourryan/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/GeodesicSlicer&diff=60722Documentation/Nightly/Modules/GeodesicSlicer2019-01-16T20:28:26Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Repetitive transcranial magnetic stimulation (rTMS) treatment for auditory hallucinations: personalized or standardized targets? Brain Stimulation, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/nourryan/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/GeodesicSlicer&diff=60721Documentation/Nightly/Modules/GeodesicSlicer2019-01-16T20:28:09Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Repetitive transcranial magnetic stimulation (rTMS) treatment for auditory hallucinations: personalized or standardized targets? Brain Stimulation, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/nourryan/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/GeodesicSlicer&diff=60720Documentation/Nightly/Modules/GeodesicSlicer2019-01-16T20:27:31Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Repetitive transcranial magnetic stimulation (rTMS) treatment for auditory hallucinations: personalized or standardized targets? Brain Stimulation, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/nourryan/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/GeodesicSlicer&diff=60719Documentation/Nightly/Modules/GeodesicSlicer2019-01-16T20:27:10Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Repetitive transcranial magnetic stimulation (rTMS) treatment for auditory hallucinations: personalized or standardized targets? Brain Stimulation, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/nourryan/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/GeodesicSlicer&diff=60718Documentation/Nightly/Modules/GeodesicSlicer2019-01-16T20:26:03Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Repetitive transcranial magnetic stimulation (rTMS) treatment for auditory hallucinations: personalized or standardized targets? Brain Stimulation, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/nourryan/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/GeodesicSlicer&diff=60717Documentation/Nightly/Modules/GeodesicSlicer2019-01-16T20:25:05Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Repetitive transcranial magnetic stimulation (rTMS) treatment for auditory hallucinations: personalized or standardized targets? Brain Stimulation, submitted</ref>.''<br />
<br />
{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/nourryan/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/GeodesicSlicer&diff=60716Documentation/Nightly/Modules/GeodesicSlicer2019-01-16T20:21:55Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Repetitive transcranial magnetic stimulation (rTMS) treatment for auditory hallucinations: personalized or standardized targets? Brain Stimulation, submitted</ref>.''<br />
<br />
{{|'''This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
__TOC__<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/nourryan/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/GeodesicSlicer&diff=60715Documentation/Nightly/Modules/GeodesicSlicer2019-01-16T20:18:59Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Repetitive transcranial magnetic stimulation (rTMS) treatment for auditory hallucinations: personalized or standardized targets? Brain Stimulation, submitted</ref>.''<br />
<br />
{{Notice|image=Stop hand nuvola.svg|'''This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br />
<br />
__TOC__<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/nourryan/SlicerGeodesic Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/GeodesicSlicer&diff=60685Documentation/Nightly/Modules/GeodesicSlicer2019-01-07T18:12:52Z<p>Frederic: Created page with "<noinclude>{{documentation/versioncheck}}</noinclude> <!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- --------------------..."</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Repetitive transcranial magnetic stimulation (rTMS) treatment for auditory hallucinations: personalized or standardized targets? Brain Stimulation, submitted</ref>.''<br />
<br />
__TOC__<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.10/Modules/GeodesicSlicer&diff=60684Documentation/4.10/Modules/GeodesicSlicer2019-01-07T18:12:25Z<p>Frederic: Created page with "<noinclude>{{documentation/versioncheck}}</noinclude> <!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- --------------------..."</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Repetitive transcranial magnetic stimulation (rTMS) treatment for auditory hallucinations: personalized or standardized targets? Brain Stimulation, submitted</ref>.''<br />
<br />
__TOC__<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.8/Modules/GeodesicSlicer&diff=60683Documentation/4.8/Modules/GeodesicSlicer2019-01-07T18:12:19Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Repetitive transcranial magnetic stimulation (rTMS) treatment for auditory hallucinations: personalized or standardized targets? Brain Stimulation, submitted</ref>.''<br />
<br />
__TOC__<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.8/Modules/GeodesicSlicer&diff=60465Documentation/4.8/Modules/GeodesicSlicer2018-10-23T18:16:16Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Repetitive transcranial magnetic stimulation (rTMS) treatment for auditory hallucinations: personalized or standardized targets? Schizophrenia Bulletin, submitted</ref>.''<br />
<br />
__TOC__<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.8/Modules/GeodesicSlicer&diff=59247Documentation/4.8/Modules/GeodesicSlicer2018-08-06T16:11:12Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Repetitive transcranial magnetic stimulation (rTMS) treatment for auditory hallucinations: personalized or standardized targets? Schizophrenia Bulletin, submitted</ref>.''<br />
<br />
__TOC__<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}<br />
# First, open 3D Slicer<br />
# Open the Slicer Extensions from the icon on the menu bar<br />
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br />
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.8/Modules/GeodesicSlicer&diff=59243Documentation/4.8/Modules/GeodesicSlicer2018-07-31T15:28:12Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Repetitive transcranial magnetic stimulation (rTMS) treatment for auditory hallucinations: personalized or standardized targets? Schizophrenia Bulletin, submitted</ref>.''<br />
<br />
__TOC__<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.8/Modules/GeodesicSlicer&diff=59241Documentation/4.8/Modules/GeodesicSlicer2018-07-30T12:01:51Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Repetitive transcranial magnetic stimulation (rTMS) treatment for auditory hallucinations: personalized or standardized targets? Schizophrenia Bulletin, submitted</ref>.''<br />
<br />
__TOC__<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii.<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.8/Modules/GeodesicSlicer&diff=59185Documentation/4.8/Modules/GeodesicSlicer2018-07-05T09:57:46Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Repetitive transcranial magnetic stimulation (rTMS) treatment for auditory hallucinations: personalized or standardized targets? Biological Psychiatry, submitted</ref>.''<br />
<br />
__TOC__<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii.<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.8/Modules/GeodesicSlicer&diff=59080Documentation/4.8/Modules/GeodesicSlicer2018-05-31T13:34:49Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Personalized or standardized target for the treatment of auditory hallucinations by rTMS? Biological Psychiatry, submitted</ref>.''<br />
<br />
__TOC__<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii.<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br />
#*Wait a moment.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.8/Modules/GeodesicSlicer&diff=59036Documentation/4.8/Modules/GeodesicSlicer2018-05-28T15:15:24Z<p>Frederic: /* rTMS resting motor threshold- Correction factor */</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Personalized or standardized target for the treatment of auditory hallucinations by rTMS? Biological Psychiatry, submitted</ref>.''<br />
<br />
__TOC__<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii.<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a mesh".<br />
#*Wait a moment.<br />
#If the segmentation is fine, press the button "Use this mesh".<br />
#*If your image was named 'T1.nii' the output will be called 'T1.stl', in the same directory of your initial image.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.8/Modules/GeodesicSlicer&diff=59035Documentation/4.8/Modules/GeodesicSlicer2018-05-28T15:14:26Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Personalized or standardized target for the treatment of auditory hallucinations by rTMS? Biological Psychiatry, submitted</ref>.''<br />
<br />
__TOC__<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii.<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a mesh".<br />
#*Wait a moment.<br />
#If the segmentation is fine, press the button "Use this mesh".<br />
#*If your image was named 'T1.nii' the output will be called 'T1.stl', in the same directory of your initial image.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7 x (SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDt-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.8/Modules/GeodesicSlicer&diff=59034Documentation/4.8/Modules/GeodesicSlicer2018-05-28T15:13:40Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Personalized or standardized target for the treatment of auditory hallucinations by rTMS? Biological Psychiatry, submitted</ref>.''<br />
<br />
__TOC__<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement.<br />
*3D printing.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii.<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a mesh".<br />
#*Wait a moment.<br />
#If the segmentation is fine, press the button "Use this mesh".<br />
#*If your image was named 'T1.nii' the output will be called 'T1.stl', in the same directory of your initial image.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7 x (SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDt-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.8/Modules/GeodesicSlicer&diff=59033Documentation/4.8/Modules/GeodesicSlicer2018-05-28T15:13:15Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Personalized or standardized target for the treatment of auditory hallucinations by rTMS? Biological Psychiatry, submitted</ref>.''<br />
<br />
__TOC__<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br />
*Surgery measurement<br />
*3D printing<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii.<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a mesh".<br />
#*Wait a moment.<br />
#If the segmentation is fine, press the button "Use this mesh".<br />
#*If your image was named 'T1.nii' the output will be called 'T1.stl', in the same directory of your initial image.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7 x (SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDt-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.8/Modules/GeodesicSlicer&diff=59032Documentation/4.8/Modules/GeodesicSlicer2018-05-28T15:07:44Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Personalized or standardized target for the treatment of auditory hallucinations by rTMS? Biological Psychiatry, submitted</ref>.''<br />
<br />
__TOC__<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry<br />
*Surgery measurement<br />
*3D printing<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii.<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a mesh".<br />
#*Wait a moment.<br />
#If the segmentation is fine, press the button "Use this mesh".<br />
#*If your image was named 'T1.nii' the output will be called 'T1.stl', in the same directory of your initial image.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7 x (SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDt-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.8/Modules/GeodesicSlicer&diff=59031Documentation/4.8/Modules/GeodesicSlicer2018-05-28T15:06:04Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Personalized or standardized target for the treatment of auditory hallucinations by rTMS? Biological Psychiatry, submitted</ref>.''<br />
<br />
__TOC__<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry<br />
*Surgery measurement<br />
*3D printing<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii.<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a mesh".<br />
#*Wait a moment.<br />
#If the segmentation is fine, press the button "Use this mesh".<br />
#*If your image was named 'T1.nii' the output will be called 'T1.stl', in the same directory of your initial image.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7 x (SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDt-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.8/Modules/GeodesicSlicer&diff=59030Documentation/4.8/Modules/GeodesicSlicer2018-05-28T15:04:45Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Personalized or standardized target for the treatment of auditory hallucinations by rTMS? Biological Psychiatry, submitted</ref>.''<br />
<br />
__TOC__<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry<br />
*Surgery measurement<br />
*3D printing<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii.<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a mesh".<br />
#*Wait a moment.<br />
#If the segmentation is fine, press the button "Use this mesh".<br />
#*If your image was named 'T1.nii' the output will be called 'T1.stl', in the same directory of your initial image.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
Run the Dijkstra's algorithm to make the 10-20 system electrode distances.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/ The nasion<br />
#* 2/ The inion <br />
#* 3/ The pre auricular to the left ear<br />
#* 4/ The pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*Project the stimulation site on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7 x (SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDt-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.8/Modules/GeodesicSlicer&diff=59029Documentation/4.8/Modules/GeodesicSlicer2018-05-28T15:02:51Z<p>Frederic: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Personalized or standardized target for the treatment of auditory hallucinations by rTMS? Biological Psychiatry, submitted</ref>.''<br />
<br />
__TOC__<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site and correct the rTMS resting motor threshold by correction factor.<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry<br />
*Surgery measurement<br />
*3D printing<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii.<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a mesh".<br />
#*Wait a moment.<br />
#If the segmentation is fine, press the button "Use this mesh".<br />
#*If your image was named 'T1.nii' the output will be called 'T1.stl', in the same directory of your initial image.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
Run the Dijkstra's algorithm to make the 10-20 system electrode distances.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/the nasion<br />
#* 2/the inion <br />
#* 3/the pre auricular to the left ear<br />
#* 4/the pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*Project the stimulation site on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7 x (SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDt-SCDm)] <br />
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The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].<br />
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<!-- ---------------------------- --></div>Frederichttps://www.slicer.org/w/index.php?title=Documentation/4.8/Modules/GeodesicSlicer&diff=59028Documentation/4.8/Modules/GeodesicSlicer2018-05-28T15:01:15Z<p>Frederic: </p>
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[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]<br />
[[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
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: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br />
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br />
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br />
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<br />
The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br />
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br />
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br />
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].<br />
* Dr. Csaba Pinter, MSc, Queen's University.<br />
* Dr. Andras Lasso, Ph.D., Queen's University.<br />
<br />
''If you use this module, please cite the following article: <ref name="Briend 2018">Briend F. et al., Personalized or standardized target for the treatment of auditory hallucinations by rTMS? Biological Psychiatry, submitted</ref>.''<br />
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__TOC__<br />
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{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp TMS site and correct the rTMS resting motor threshold by correction factor<br />
<br />
'''Terminology'''<br />
*'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br />
*'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br />
*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br />
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The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br />
*Stimulation in psychiatry<br />
*Surgery measurement<br />
*3D printing<br />
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{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
==== Create a mesh ====<br />
[[File:Create mesh.png|thumb|right]]<br />
<br />
A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br />
<br />
# Load a volume.nii.<br />
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br />
# Press the button "Create a mesh".<br />
#*Wait a moment.<br />
#If the segmentation is fine, press the button "Use this mesh".<br />
#*If your image was named 'T1.nii' the output will be called 'T1.stl', in the same directory of your initial image.<br />
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br />
<br />
==== Parameters to find the shortest path ====<br />
[[File:Shortest past.png|thumb|right]]<br />
<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br />
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br />
#** Length (cm): The length of the current curve is shown in centimeter.<br />
<br />
====10-20 system electrode====<br />
Run the Dijkstra's algorithm to make the 10-20 system electrode distances.<br />
<br />
[[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br />
# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br />
#* 1/the nasion<br />
#* 2/the inion <br />
#* 3/the pre auricular to the left ear<br />
#* 4/the pre auricular to the right ear<br />
# Input STL model: The model you use (after "use this mesh", the T1.stl created).<br />
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br />
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br />
<br />
*Project the stimulation site on the 10-20 system electrode distances and characterize it.<br />
# Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br />
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3nearest electrodes around it.<br />
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br />
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br />
<br />
<br />
====rTMS resting motor threshold- Correction factor====<br />
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br />
<br />
[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br />
<br />
# M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br />
# Set the stimulation intensity of the resting motor threshold.<br />
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br />
#* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br />
#* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7 x (SCDx - SCDm) + rMT] <br />
#* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDt-SCDm)] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
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{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Frederic