Documentation/Nightly/Modules/GeodesicSlicer - Revision history

Frederic: add DOI

2020-10-16T09:30:16Z

add DOI

Frederic at 09:57, 12 March 2020

2020-03-12T09:57:51Z

Frederic at 10:24, 20 December 2019

2019-12-20T10:24:43Z

Frederic at 17:08, 17 September 2019

2019-09-17T17:08:37Z

Frederic at 17:07, 17 September 2019

2019-09-17T17:07:53Z

Frederic at 15:38, 17 September 2019

2019-09-17T15:38:57Z

Frederic at 15:48, 16 September 2019

2019-09-16T15:48:42Z

Frederic at 20:54, 11 September 2019

2019-09-11T20:54:56Z

Frederic at 21:41, 4 September 2019

2019-09-04T21:41:37Z

Frederic at 18:44, 4 September 2019

2019-09-04T18:44:15Z

@@ Line 26: / Line 26: @@
 *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>.''
+''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.}}

@@ Line 26: / Line 26: @@
 *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>.''
+''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.}}

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-<noinclude>{{documentation/versioncheck}}</noinclude>
+<noinclude>{{documentation/versioncheck}}
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 {{documentation/{{documentation/version}}/module-header}}
@@ Line 18: / Line 19: @@
 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 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>.''
+''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.}}
@@ Line 35: / Line 36: @@
 '''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>
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 {{documentation/{{documentation/version}}/module-section|Installation}}
 # 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.
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 {{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.
@@ Line 56: / Line 60: @@
 {{documentation/{{documentation/version}}/module-section|Panels and their use}}
-==== Create a mesh ====
+====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).
+#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.
 #Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.
-==== Parameters to find the shortest path ====
+====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).
+#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).
+#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.
 ====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
+#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!):
-#* 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 10-20 EEG system electrode" to draw the 10-20 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 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.
 *'''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.
+#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'.
-#* 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.
@@ Line 102: / Line 109: @@
 [[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].
+#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.
+#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 scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1.
+#*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]
+#*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)]
+#*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)]
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 {{documentation/{{documentation/version}}/module-footer}}
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@@ Line 25: / Line 25: @@
 * 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>.''
+''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.}}

@@ Line 25: / Line 25: @@
 * 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>.''
+''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.}}

@@ Line 111: / Line 111: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/extension-section|Information for Developers}}
-The code is available at [https://github.com/nourryan/SlicerGeodesic Github].
+The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].
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