Documentation/4.11/Modules/GeodesicSlicer - Revision history

https://www.slicer.org/w/index.php?action=history&feed=atom&title=Documentation%2F4.11%2FModules%2FGeodesicSlicer Documentation/4.11/Modules/GeodesicSlicer - Revision history 2026-04-06T23:43:48Z Revision history for this page on the wiki MediaWiki 1.33.0 https://www.slicer.org/w/index.php?title=Documentation/4.11/Modules/GeodesicSlicer&diff=63899&oldid=prev Frederic at 10:23, 16 December 2021 2021-12-16T10:23:58Z

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Frederic https://www.slicer.org/w/index.php?title=Documentation/4.11/Modules/GeodesicSlicer&diff=63898&oldid=prev Frederic: Created page with "<noinclude>{{documentation/versioncheck}}</noinclude>  {{documentation/{{documentation/version}}/module-header}} <!-- -----------------..." 2021-12-16T10:22:12Z

<p>Created page with "<noinclude>{{documentation/versioncheck}}</noinclude>  {{documentation/{{documentation/version}}/module-header}} <br /> {{documentation/{{documentation/version}}/module-header}}<br /> <br /> [[File:GeodesicSlicer logo.png|128x128px|thumb|left|]]<br /> [[File:Screen-shot of the GeodesicSlicer program. .png|thumb|right|The users enters 1) the T1-weighted whole-brain anatomical image 2) Place four points: the nasion, the inion, the left tragus and the right tragus. The program make a 3D mesh morphed to the structural MRI data of a participant and calculates the 10-20 system EEG with T3P3, and outputs the distance between the anatomical target and the T3 electrode.]]<br /> <br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> : '''Author(s)/Contributor(s):''' Frederic Briend (ISTS EA 7466, UNICAEN), Antoine Nourry (UMS 3408)<br><br /> : '''Acknowledgements:''' This work was supported by a Perceneige-Fondamental prize, CHU Caen, Region Normandie and UNICAEN.<br><br /> : '''Contact:''' Frederic Briend, <email>briend@cyceron.fr</email><br><br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> The module has been developed based on ideas and feedbacks from the community. We would like to especially thank:<br /> <br /> * Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.<br /> * Dr. Clément Nathou, M.D., Ph.D., CHU de Caen.<br /> * Dr. Nicolas Delcroix, Ph.D., UMS 3408.<br /> * Dr. Sonia Dollfus, M.D., Ph.D., CHU de Caen, header of [http://www.ists.cyceron.fr/ ISTS].<br /> * Dr. Csaba Pinter, MSc, Queen's University.<br /> * Dr. Andras Lasso, Ph.D., Queen's University.<br /> <br /> ''If you use this module, please cite the following article: <ref name="Briend 2020a">Briend F. et al., A new toolbox to compare NIBS localization method: Application for auditory hallucinations in schizophrenia. Schizophrenia Research, https://doi.org/10.1016/j.schres.2020.09.001</ref> and <ref name="Briend 2020b">Briend F. et al., GeodesicSlicer: a Slicer Toolbox for Targeting Brain Stimulation. Neuroinformatics. https://doi.org/10.1007/s12021-020-09457-9</ref>.''<br /> <br /> {{Warning |This extension is under the [http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html CeCill license], a copyleft license.}}<br /> <br /> __TOC__<br /> <br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module can draw an EEG 10-20 system, determine the projected scalp stimulation site (MRI guided brain stimulation without the use of a neuronavigation System) and correct the rTMS resting motor threshold by correction factor.<br /> <br /> '''Terminology'''<br /> *'''''Mesh''''' A mesh or polygon mesh is a collection of vertices, edges and faces that defines the shape of a polyhedral object in 3D computer graphics and solid modeling.<br /> *'''''Shortest path''''' In graph theory, the shortest path problem is the problem of finding a path between two vertices (or nodes) in a graph such that the sum of the weights of its constituent edges is minimized.<br /> *'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and to correlate external skull locations with underlying cortical areas.<ref name="Jasper 1958">Jasper, H. (1958). The ten twenty electrode system of the international federation. Electroencephalography and Clinical Neurophysiology, 10, 371‑375.</ref> <br /> <br /> <br /> {{documentation/{{documentation/version}}/module-section|Installation}}<br /> # First, open 3D Slicer<br /> # Open the Slicer Extensions from the icon on the menu bar<br /> # Choose "Geodesic Slicer" module from the list of extensions and click "INSTALL" button.<br /> # Once you restart 3D Slicer, the Geodesic Slicer module should show up on the Modules menu (under Informatics->Geodesic Slicer) <br /> <br /> <br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> The overall goal is to allow users to find the shortest paths between nodes in a graph and via the Dijkstra's algorithm to make 10-20 system. This module can be used for:<br /> *Stimulation in psychiatry: MRI guided brain stimulation without the use of a neuronavigation system.<br /> *Surgery measurement.<br /> *3D printing.<br /> <br /> <br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> ==== Create a mesh ====<br /> [[File:Create mesh.png|thumb|right]]<br /> <br /> A typical straightforward Geodesic Slicer workflow for consists of the following steps:<br /> <br /> # Load a volume.nii (by Drag & Drop or the Add Data dialogue).<br /> # Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.<br /> # Press the button "Create a quick mesh" or "Create a mesh" (with filling holes smoothing, better for the next part but longer).<br /> #*Wait a moment.<br /> #Go to '''Parameters to find the shortest path''' or '''Make 10-20 EEG system electrode''' section.<br /> <br /> ==== Parameters to find the shortest path ====<br /> [[File:Shortest past.png|thumb|right]]<br /> <br /> # Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). <br /> # Input STL model: The model you use (after "use this mesh", the T1.stl created).<br /> #* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.<br /> #* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.<br /> #** Length (cm): The length of the current curve is shown in centimeter.<br /> <br /> ====10-20 system electrode====<br /> *Run the Dijkstra's algorithm to '''make the 10-20 system electrode'''.<br /> <br /> [[File:4 landmarks.png|thumb|right|Four anatomical landmarks are used for the essential positioning of the electrodes: the nasion, the inion, the pre auricular to the left ear and the pre auricular to the right ear. ]]<br /> # 4 anatomical landmarks: (Sources Points) The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above). Four anatomical landmarks are used for the essential positioning of the electrodes (in this order!):<br /> #* 1/ The nasion<br /> #* 2/ The inion <br /> #* 3/ The pre auricular to the left ear<br /> #* 4/ The pre auricular to the right ear<br /> # Input STL model: The model you use (after "use this mesh", the T1.stl created).<br /> # Press the button "Make 10-20 EEG system electrode" to draw the 10-20 EEG system via the Dijkstra's algorithm.<br /> #* The traditional T3P3 site according to the International 10–20 system of electroencephalogram was identified.<br /> <br /> *'''Project the stimulation site''' on the 10-20 system electrode distances and characterize it.<br /> # Stimulation Site placed: Place on the T1-weighted anatomical image the stimulation point that you want since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'.<br /> # Press the button "Project the stimulation site" to project the stimulation point on the scalp and find the 3 nearest electrodes around it.<br /> #* Nearest electrode 1: The distance in centimeter between the first nearest electrode and the projected stimulation site.<br /> #* Nearest electrode 2: The distance in centimeter between the second nearest electrode and the projected stimulation site.<br /> #* Nearest electrode 3: The distance in centimeter between the third nearest electrode and the projected stimulation site.<br /> <br /> <br /> ====rTMS resting motor threshold- Correction factor====<br /> Calculate correction factors to adjust the rTMS dose for the treatment (according to the depth of the stimulation site).<br /> <br /> [[File:M1.png|thumb|Localization of the motor hand area via a knob on the precentral gyrus]]<br /> <br /> # M1 Point Placed: Place on the T1-weighted anatomical image a point targeting the human [https://en.wikipedia.org/wiki/Motor_cortex|motor motor cortex] since the "Create-and-place Fiducial" button. Once this point given, click on 'Yes'. Help via the [https://pdfs.semanticscholar.org/ba38/045e9f01ec4d128c5fbe5a46dc209fccaac4.pdf Yousry's method].<br /> # Set the stimulation intensity of the resting motor threshold.<br /> # Press the button "Correct the motor threshold" to correct the unadjusted motor threshold (rMT) in % stimulator output.<br /> #* Two adjusted motor threshold (AdjMT%) in % stimulator output are given where SCDx is the scalp-to-cortex distance between the scalp and and the Stimulation Site, SCDm is the scalp-to-cortex distance between the scalp and M1. <br /> #* 1/ The first according to Stokes et al. Clin Neurophysiol 2007 <ref name="Stokes 2007">Stokes, M. G., Chambers, C. D., Gould, I. C., English, T., McNaught, E., McDonald, O., & Mattingley, J. B. (2007). Distance-adjusted motor threshold for transcranial magnetic stimulation. Clinical Neurophysiology, 118(7), 1617‑1625.</ref> , where [AdjMT% = 2,7*(SCDx - SCDm) + rMT] <br /> #* 2/ The second according to Hoffman et al. Biol Psychiatry 2013 <ref name="Hoffman 2013">Hoffman, R. E., Wu, K., Pittman, B., Cahill, J. D., Hawkins, K. A., Fernandez, T., & Hannestad, J. (2013). Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail « voices »: a randomized trial. Biological Psychiatry, 73(10), 1008‑1014. </ref> , where [AdjMT% = 0.90*rMT*e0.036*(SCDx-SCDm)] <br /> <br /> <br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> The code is available at [https://github.com/FredericBr/SlicerGeodesic Github].<br /> <br /> <br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> <br /> <br /> {{documentation/{{documentation/version}}/module-footer}}<br /> </div>

Frederic