Difference between revisions of "Documentation/Nightly/Modules/GeodesicSlicer"
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The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:  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. Olivier Etard, M.D., Ph.D., CHU de Caen. 
−  * Dr. Clément Nathou, 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. 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. 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. Csaba Pinter, MSc, Queen's University. 
−  * Dr. Andras Lasso, Ph.D., Queen's University.  +  *Dr. Andras Lasso, Ph.D., Queen's University. 
−  ''If you use this module, please cite the following article: <ref name="Briend  +  ''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/s12021020094579</ref>.'' 
{{Warning This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1en.html CeCill license], a copyleft license.}}  {{Warning This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1en.html CeCill license], a copyleft license.}}  
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'''Terminology'''  '''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.  *'''''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.  *'''''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.  
−  *'''''1020 EEG system''''' The International 1020 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>  +  *'''''1020 EEG system''''' The International 1020 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> 
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−  # First, open 3D Slicer  +  
−  # Open the Slicer Extensions from the icon on the menu bar  +  #First, open 3D Slicer 
−  # Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.  +  #Open the Slicer Extensions from the icon on the menu bar 
−  # Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics>Geodesic Slicer)  +  #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)  
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{{documentation/{{documentation/version}}/modulesectionUse Cases}}  {{documentation/{{documentation/version}}/modulesectionUse 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 1020 system. This module can be used for:  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 1020 system. This module can be used for:  
+  
*Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.  *Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.  
*Surgery measurement.  *Surgery measurement.  
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{{documentation/{{documentation/version}}/modulesectionPanels and their use}}  {{documentation/{{documentation/version}}/modulesectionPanels and their use}}  
−  ==== Create a mesh ====  +  ====Create a mesh==== 
[[File:Create mesh.pngthumbright]]  [[File:Create mesh.pngthumbright]]  
A typical straightforward Geodesic Slicer workflow for consists of the following steps:  A typical straightforward Geodesic Slicer workflow for consists of the following steps:  
−  # Load a volume.nii (by Drag & Drop or the Add Data dialogue).  +  #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.  +  #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).  +  #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.  #*Wait a moment.  
#Go to '''Parameters to find the shortest path''' or '''Make 1020 EEG system electrode''' section.  #Go to '''Parameters to find the shortest path''' or '''Make 1020 EEG system electrode''' section.  
−  ==== Parameters to find the shortest path ====  +  ====Parameters to find the shortest path==== 
[[File:Shortest past.pngthumbright]]  [[File:Shortest past.pngthumbright]]  
−  # Source points: The list of fiducial points on the curve, since the "Createandplace Fiducial" button (in green in the figure above).  +  #Source points: The list of fiducial points on the curve, since the "Createandplace Fiducial" button (in green in the figure above). 
−  # Input STL model: The model you use (after "use this mesh", the T1.stl created).  +  #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.  +  #*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.  +  #*Draw the shortest path: Draw the Dijkstra's algorithm shortest path. 
−  #** Length (cm): The length of the current curve is shown in centimeter.  +  #**Length (cm): The length of the current curve is shown in centimeter. 
====1020 system electrode====  ====1020 system electrode====  
+  
*Run the Dijkstra's algorithm to '''make the 1020 system electrode'''.  *Run the Dijkstra's algorithm to '''make the 1020 system electrode'''.  
[[File:4 landmarks.pngthumbrightFour 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. ]]  [[File:4 landmarks.pngthumbrightFour 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 "Createandplace 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  +  #4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Createandplace Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!): 
−  #* 2/ The inion  +  #*1/ The nasion 
−  #* 3/ The pre auricular to the left ear  +  #*2/ The inion 
−  #* 4/ The pre auricular to the right ear  +  #*3/ The pre auricular to the left ear 
−  # Input STL model: The model you use (after "use this mesh", the T1.stl created).  +  #*4/ The pre auricular to the right ear 
−  # Press the button "Make 1020 EEG system electrode" to draw the 1020 EEG system via the Dijkstra's algorithm.  +  #Input STL model: The model you use (after "use this mesh", the T1.stl created). 
−  #* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.  +  #Press the button "Make 1020 EEG system electrode" to draw the 1020 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 1020 system electrode distances and characterize it.  *'''Project the stimulation site''' on the 1020 system electrode distances and characterize it.  
−  # Stimulation Site placed: Place on the T1weighted anatomical image the stimulation point that you want since the "Createandplace 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.  +  #Stimulation Site placed: Place on the T1weighted anatomical image the stimulation point that you want since the "Createandplace Fiducial" button. Once this point given, click on 'Yes'. 
−  #* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.  +  #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 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.  +  #*Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site. 
−  #* Nearest electrode 3: The distance in centimeter between the third 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.  
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[[File:M1.pngthumbLocalization of the motor hand area via a knob on the precentral gyrus]]  [[File:M1.pngthumbLocalization of the motor hand area via a knob on the precentral gyrus]]  
−  # M1 Point Placed: Place on the T1weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortexmotor motor cortex] since the "Createandplace Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].  +  #M1 Point Placed: Place on the T1weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortexmotor motor cortex] since the "Createandplace 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.  +  #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.  +  #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 scalptocortex distance between the scalp and and the Stimulation Site, SCDm is the scalptocortex distance between the scalp and M1.  +  #*Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalptocortex distance between the scalp and and the Stimulation Site, SCDm is the scalptocortex 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). Distanceadjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx  SCDm) + rMT]  +  #*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). Distanceadjusted 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*(SCDxSCDm)]  +  #*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*(SCDxSCDm)] 
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Latest revision as of 09:57, 12 March 2020
Home < Documentation < Nightly < Modules < GeodesicSlicer
For the stable Slicer documentation, visit the 4.10 page. 
Introduction and Acknowledgements

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 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: ^{[1]} and ^{[2]}.
Warning:  This extension is under the CeCill license, a copyleft license. 
Module Description
This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 1020 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.
 1020 EEG system The International 1020 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.^{[3]}
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)
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 1020 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.
Panels and their use
Create a mesh
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 1020 EEG system electrode section.
Parameters to find the shortest path
 Source points: The list of fiducial points on the curve, since the "Createandplace 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.
1020 system electrode
 Run the Dijkstra's algorithm to make the 1020 system electrode.
 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Createandplace 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 1020 EEG system electrode" to draw the 1020 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 1020 system electrode distances and characterize it.
 Stimulation Site placed: Place on the T1weighted anatomical image the stimulation point that you want since the "Createandplace 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).
 M1 Point Placed: Place on the T1weighted anatomical image a point targeting the human motor cortex since the "Createandplace Fiducial" button. Once this point given, click on 'Yes'. Help via the 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 scalptocortex distance between the scalp and and the Stimulation Site, SCDm is the scalptocortex distance between the scalp and M1.
 1/ The first according to Stokes et al. Clin Neurophysiol 2007 ^{[4]} , where [AdjMT% = 2,7*(SCDx  SCDm) + rMT]
 2/ The second according to Hoffman et al. Biol Psychiatry 2013 ^{[5]} , where [AdjMT% = 0.90*rMT*e0.036*(SCDxSCDm)]
Information for Developers
The code is available at Github.
References
 ↑ Briend F. et al., A new toolbox to compare NIBS localization method: Application for auditory hallucinations in schizophrenia. Schizophrenia Research, submitted
 ↑ Briend F. et al., GeodesicSlicer: a Slicer Toolbox for Targeting Brain Stimulation. Neuroinformatics. https://doi.org/10.1007/s12021020094579
 ↑ Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.
 ↑ Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distanceadjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.
 ↑ 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.