Slicer Wiki - User contributions [en]

Documentation/4.11/Modules/GeodesicSlicer

2021-12-16T10:23:58Z

Frederic:

<noinclude>{{documentation/versioncheck}}
</noinclude>

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]


:'''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
:'''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
:'''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

*Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
*Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
*Dr. Nicolas Delcroix, Ph.D., UMS 3408.
*Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/ ISTS].
*Dr. Csaba Pinter, MSc, Queen's University.
*Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__


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.

'''Terminology'''

*'''''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.
*'''''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.
*'''''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>


#First, open 3D Slicer
#Open the Slicer Extensions from the icon on the menu bar
#Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
#Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


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:

*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.

====Create a mesh====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

#Load a volume.nii (by Drag & Drop or the Add Data dialogue).
#Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
#Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

====Parameters to find the shortest path====
[[File:Shortest past.png|thumb|right]]

#Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
#Input STL model: The model you use (after "use this mesh", the T1.stl created).
#*Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#*Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#**Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====

*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]

#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!):
#*1/ The nasion
#*2/ The inion
#*3/ The pre auricular to the left ear
#*4/ The pre auricular to the right ear
#Input STL model: The model you use (after "use this mesh", the T1.stl created).
#Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#*The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.

#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'.
#Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#*Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#*Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#*Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

#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].
#Set the stimulation intensity of the resting motor threshold.
#Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#*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.
#*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]
#*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)]


The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].


 <references />

Documentation/4.11/Modules/GeodesicSlicer

2021-12-16T10:22:12Z

Frederic: Created page with "<noinclude>{{documentation/versioncheck}}</noinclude>  {{documentation/{{documentation/version}}/module-header}} <!-- -----------------..."

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/ ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.10/Modules/GeodesicSlicer

2020-10-16T09:31:15Z

Frederic: add DOI

Documentation/Nightly/Modules/GeodesicSlicer

2020-10-16T09:30:16Z

Frederic: add DOI

<noinclude>{{documentation/versioncheck}}
</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

*Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
*Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
*Dr. Nicolas Delcroix, Ph.D., UMS 3408.
*Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
*Dr. Csaba Pinter, MSc, Queen's University.
*Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''

*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation}}

#First, open 3D Slicer
#Open the Slicer Extensions from the icon on the menu bar
#Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
#Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:

*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

====Create a mesh====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

#Load a volume.nii (by Drag & Drop or the Add Data dialogue).
#Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
#Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

====Parameters to find the shortest path====
[[File:Shortest past.png|thumb|right]]

#Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
#Input STL model: The model you use (after "use this mesh", the T1.stl created).
#*Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#*Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#**Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====

*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]

#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!):
#*1/ The nasion
#*2/ The inion
#*3/ The pre auricular to the left ear
#*4/ The pre auricular to the right ear
#Input STL model: The model you use (after "use this mesh", the T1.stl created).
#Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#*The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.

#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'.
#Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#*Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#*Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#*Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

#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].
#Set the stimulation intensity of the resting motor threshold.
#Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#*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.
#*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]
#*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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

<references />

Documentation/Nightly/Modules/GeodesicSlicer

2020-03-12T09:57:51Z

Frederic:

<noinclude>{{documentation/versioncheck}}
</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

*Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
*Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
*Dr. Nicolas Delcroix, Ph.D., UMS 3408.
*Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
*Dr. Csaba Pinter, MSc, Queen's University.
*Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''

*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation}}

#First, open 3D Slicer
#Open the Slicer Extensions from the icon on the menu bar
#Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
#Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:

*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

====Create a mesh====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

#Load a volume.nii (by Drag & Drop or the Add Data dialogue).
#Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
#Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

====Parameters to find the shortest path====
[[File:Shortest past.png|thumb|right]]

#Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
#Input STL model: The model you use (after "use this mesh", the T1.stl created).
#*Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#*Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#**Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====

*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]

#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!):
#*1/ The nasion
#*2/ The inion
#*3/ The pre auricular to the left ear
#*4/ The pre auricular to the right ear
#Input STL model: The model you use (after "use this mesh", the T1.stl created).
#Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#*The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.

#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'.
#Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#*Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#*Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#*Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

#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].
#Set the stimulation intensity of the resting motor threshold.
#Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#*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.
#*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]
#*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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

<references />

Documentation/4.10/Modules/GeodesicSlicer

2020-03-12T09:56:25Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/ ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.10/Modules/GeodesicSlicer

2019-12-20T10:25:10Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/ ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/GeodesicSlicer

2019-12-20T10:24:43Z

Frederic:

<noinclude>{{documentation/versioncheck}}
</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

*Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
*Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
*Dr. Nicolas Delcroix, Ph.D., UMS 3408.
*Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
*Dr. Csaba Pinter, MSc, Queen's University.
*Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''

*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation}}

#First, open 3D Slicer
#Open the Slicer Extensions from the icon on the menu bar
#Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
#Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:

*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

====Create a mesh====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

#Load a volume.nii (by Drag & Drop or the Add Data dialogue).
#Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
#Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

====Parameters to find the shortest path====
[[File:Shortest past.png|thumb|right]]

#Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
#Input STL model: The model you use (after "use this mesh", the T1.stl created).
#*Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#*Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#**Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====

*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]

#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!):
#*1/ The nasion
#*2/ The inion
#*3/ The pre auricular to the left ear
#*4/ The pre auricular to the right ear
#Input STL model: The model you use (after "use this mesh", the T1.stl created).
#Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#*The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.

#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'.
#Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#*Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#*Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#*Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

#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].
#Set the stimulation intensity of the resting motor threshold.
#Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#*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.
#*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]
#*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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

<references />

Documentation/4.10/Modules/GeodesicSlicer

2019-09-17T17:09:20Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/ ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/GeodesicSlicer

2019-09-17T17:08:37Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/GeodesicSlicer

2019-09-17T17:07:53Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/GeodesicSlicer

2019-09-17T15:38:57Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.10/Modules/GeodesicSlicer

2019-09-16T15:49:09Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/ ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/GeodesicSlicer

2019-09-16T15:48:42Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.10/Modules/GeodesicSlicer

2019-09-11T20:55:35Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/ ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/GeodesicSlicer

2019-09-11T20:54:56Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/GeodesicSlicer

2019-09-04T21:41:37Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/GeodesicSlicer

2019-09-04T18:44:15Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/nourryan/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.10/Modules/GeodesicSlicer

2019-09-04T18:32:56Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/ ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.10/Modules/GeodesicSlicer

2019-07-18T20:32:01Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/ ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.10/Modules/GeodesicSlicer

2019-07-18T20:30:03Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.10/Modules/GeodesicSlicer

2019-07-15T16:38:16Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.10/Modules/GeodesicSlicer

2019-01-16T20:29:20Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/GeodesicSlicer

2019-01-16T20:28:40Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/nourryan/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/GeodesicSlicer

2019-01-16T20:28:26Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/nourryan/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/GeodesicSlicer

2019-01-16T20:28:09Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/nourryan/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/GeodesicSlicer

2019-01-16T20:27:31Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/nourryan/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/GeodesicSlicer

2019-01-16T20:27:10Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/nourryan/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/GeodesicSlicer

2019-01-16T20:26:03Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:

* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}
__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/nourryan/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/GeodesicSlicer

2019-01-16T20:25:05Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}

__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/nourryan/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/GeodesicSlicer

2019-01-16T20:21:55Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{|'''This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}
__TOC__

{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/nourryan/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/GeodesicSlicer

2019-01-16T20:18:59Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

{{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.}}

__TOC__


{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/nourryan/SlicerGeodesic Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/GeodesicSlicer

2019-01-07T18:12:52Z

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

__TOC__


{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.10/Modules/GeodesicSlicer

2019-01-07T18:12:25Z

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

__TOC__


{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.8/Modules/GeodesicSlicer

2019-01-07T18:12:19Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

__TOC__


{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.8/Modules/GeodesicSlicer

2018-10-23T18:16:16Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Nicolas Delcroix, Ph.D., UMS 3408.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

__TOC__


{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.8/Modules/GeodesicSlicer

2018-08-06T16:11:12Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

__TOC__


{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Installation (in progress)}}
# First, open 3D Slicer
# Open the Slicer Extensions from the icon on the menu bar
# Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.
# Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer)


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.8/Modules/GeodesicSlicer

2018-07-31T15:28:12Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

__TOC__


{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii (by Drag & Drop or the Add Data dialogue).
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.8/Modules/GeodesicSlicer

2018-07-30T12:01:51Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

__TOC__


{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii.
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.8/Modules/GeodesicSlicer

2018-07-05T09:57:46Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

__TOC__


{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii.
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.8/Modules/GeodesicSlicer

2018-05-31T13:34:49Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

__TOC__


{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii.
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).
#*Wait a moment.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.8/Modules/GeodesicSlicer

2018-05-28T15:15:24Z

Frederic: /* rTMS resting motor threshold- Correction factor */

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

__TOC__


{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii.
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a mesh".
#*Wait a moment.
#If the segmentation is fine, press the button "Use this mesh".
#*If your image was named 'T1.nii' the output will be called 'T1.stl', in the same directory of your initial image.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.8/Modules/GeodesicSlicer

2018-05-28T15:14:26Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

__TOC__


{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii.
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a mesh".
#*Wait a moment.
#If the segmentation is fine, press the button "Use this mesh".
#*If your image was named 'T1.nii' the output will be called 'T1.stl', in the same directory of your initial image.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.8/Modules/GeodesicSlicer

2018-05-28T15:13:40Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

__TOC__


{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement.
*3D printing.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii.
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a mesh".
#*Wait a moment.
#If the segmentation is fine, press the button "Use this mesh".
#*If your image was named 'T1.nii' the output will be called 'T1.stl', in the same directory of your initial image.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.8/Modules/GeodesicSlicer

2018-05-28T15:13:15Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

__TOC__


{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.
*Surgery measurement
*3D printing


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii.
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a mesh".
#*Wait a moment.
#If the segmentation is fine, press the button "Use this mesh".
#*If your image was named 'T1.nii' the output will be called 'T1.stl', in the same directory of your initial image.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.8/Modules/GeodesicSlicer

2018-05-28T15:07:44Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

__TOC__


{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry
*Surgery measurement
*3D printing


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii.
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a mesh".
#*Wait a moment.
#If the segmentation is fine, press the button "Use this mesh".
#*If your image was named 'T1.nii' the output will be called 'T1.stl', in the same directory of your initial image.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.8/Modules/GeodesicSlicer

2018-05-28T15:06:04Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

__TOC__


{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry
*Surgery measurement
*3D printing


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii.
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a mesh".
#*Wait a moment.
#If the segmentation is fine, press the button "Use this mesh".
#*If your image was named 'T1.nii' the output will be called 'T1.stl', in the same directory of your initial image.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
*Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.8/Modules/GeodesicSlicer

2018-05-28T15:04:45Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

__TOC__


{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry
*Surgery measurement
*3D printing


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii.
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a mesh".
#*Wait a moment.
#If the segmentation is fine, press the button "Use this mesh".
#*If your image was named 'T1.nii' the output will be called 'T1.stl', in the same directory of your initial image.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
Run the Dijkstra's algorithm to make the 10-20 system electrode distances.

[[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. ]]
# 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!):
#* 1/ The nasion
#* 2/ The inion
#* 3/ The pre auricular to the left ear
#* 4/ The pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*Project the stimulation site on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.8/Modules/GeodesicSlicer

2018-05-28T15:02:51Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-end}}

The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

__TOC__


{{documentation/{{documentation/version}}/module-section|Module Description}}
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.

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry
*Surgery measurement
*3D printing


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii.
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a mesh".
#*Wait a moment.
#If the segmentation is fine, press the button "Use this mesh".
#*If your image was named 'T1.nii' the output will be called 'T1.stl', in the same directory of your initial image.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
Run the Dijkstra's algorithm to make the 10-20 system electrode distances.

[[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. ]]
# 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!):
#* 1/the nasion
#* 2/the inion
#* 3/the pre auricular to the left ear
#* 4/the pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*Project the stimulation site on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-footer}}

Documentation/4.8/Modules/GeodesicSlicer

2018-05-28T15:01:15Z

Frederic:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:GeodesicSlicer logo.png|128x128px|thumb|left|GeodesicSlicer logo]]
[[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.]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
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: '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408) 
: '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN. 
: '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email> 
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The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:
* Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
* Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.
* Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/spip.php?rubrique17 ISTS].
* Dr. Csaba Pinter, MSc, Queen's University.
* Dr. Andras Lasso, Ph.D., Queen's University.

''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>.''

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{{documentation/{{documentation/version}}/module-section|Module Description}}
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

'''Terminology'''
*'''''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.
*'''''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.
*'''''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>


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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:
*Stimulation in psychiatry
*Surgery measurement
*3D printing


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==== Create a mesh ====
[[File:Create mesh.png|thumb|right]]

A typical straightforward Geodesic Slicer workflow for consists of the following steps:

# Load a volume.nii.
# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
# Press the button "Create a mesh".
#*Wait a moment.
#If the segmentation is fine, press the button "Use this mesh".
#*If your image was named 'T1.nii' the output will be called 'T1.stl', in the same directory of your initial image.
#Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.

==== Parameters to find the shortest path ====
[[File:Shortest past.png|thumb|right]]

# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
#** Length (cm): The length of the current curve is shown in centimeter.

====10-20 system electrode====
Run the Dijkstra's algorithm to make the 10-20 system electrode distances.

[[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. ]]
# 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!):
#* 1/the nasion
#* 2/the inion
#* 3/the pre auricular to the left ear
#* 4/the pre auricular to the right ear
# Input STL model: The model you use (after "use this mesh", the T1.stl created).
# Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
#* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.

*Project the stimulation site on the 10-20 system electrode distances and characterize it.
# 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'.
# Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3nearest electrodes around it.
#* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.
#* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.
#* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.

====rTMS resting motor threshold- Correction factor====
Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).

[[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]

# 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].
# Set the stimulation intensity of the resting motor threshold.
# Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.
#* 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.
#* 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]
#* 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)]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
The code is available at [https://github.com/FredericBr/GeodesicPathSlicer Github].


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