Difference between revisions of "Documentation/4.8/Modules/GeodesicSlicer"

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*'''''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.
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*'''''10-20 EEG system''''' The International 10-20 system is commonly used for EEG electrode placement and for correlating external skull locations to underlying cortical areas.<ref name="Jasper 1958">Jasper, H.H. The ten-twenty electrode system of the International Federation. Electroencephalogr. Clin. Neurophysiol., 1958, 10: 370-375</ref>  
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*'''''10-20 EEG system''''' The International 10-20 system is commonly used for electroencephalogram (EEG) electrode placement and for correlating external skull locations to underlying cortical areas.<ref name="Jasper 1958">Jasper, H.H. The ten-twenty electrode system of the International Federation. Electroencephalogr. Clin. Neurophysiol., 1958, 10: 370-375</ref>  
  
 
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{{documentation/{{documentation/version}}/module-section|Panels and their use}}
 
{{documentation/{{documentation/version}}/module-section|Panels and their use}}
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[[File:Wiki main picture.png|thumb|center|Geodesic Slicer. Panel set]]
 
  
 
==== Create a mesh ====
 
==== Create a mesh ====
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[[File:Create mesh.png|thumb|center]]
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Image à insérer: "wiki_main_picture2.png"
 
  
 
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.
 
# Load a volume.nii.
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# Enter the Geodesic Slicer module using either the toolbar or the Modules menu button.
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# Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
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# Create a mesh.
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# Press the button "Create a mesh".
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#*Wait a moment
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#*Wait a moment.
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#Use this mesh.
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#If the segmentation is fine, press the button "Use this mesh".
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#*If your background was named 't1' the label will be called 't1-label'.
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#*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.
 
#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 ====
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# Source points.
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[[File:Shortest past.png|thumb|center]]
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# Input STL model.
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#* Calculate in centimeter the shortest path via the Dijkstra's algorithm.
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# Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).  
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#* Draw the Dijkstra's algorithm shortest path.
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# Input STL model: The model you use (after "use this mesh", the t1.stl created).
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#** Length (cm)
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#* Find the shortest path: Calculate in centimeter the geodesic (shortest) path via the Dijkstra's algorithm.
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#* Draw the shortest path: Draw the Dijkstra's algorithm shortest path.
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#** Length (cm): The length of the current curve is shown in centimeter.
  
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==10-20 system electrode==
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====10-20 system electrode====
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Run the Dijkstra's algorithm to make the 10-20 system electrode distances
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Run the Dijkstra's algorithm to make the 10-20 system electrode distances.
  
 
===4 anatomical landmarks===
 
===4 anatomical landmarks===
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Four anatomical landmarks are used for the essential positioning of the electrodes:
 
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* 1/the nasion
 
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* 2/the inion
 
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* 3/the pre auricular to the left ear
 
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* 4/the pre auricular to the right ear
 
  
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===Input STL model===
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# 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!):
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This model required to contain a dense set of points.
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#* 1/the nasion
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#* 2/the inion
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[[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. ]]
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#* 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 and an anatomical target defined as the site for which stimulation was found to produce the most significant effects on AVH and was located in the left temporo-parietal cortex <ref name="Hoffman 2013">Hoffman RE. et al., Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail “voices”: a randomized trial. Biol Psychiatry 2013;73:1008–14</ref> <ref name="Dollfus 2017">Dollfus S. et al., Efficacy of high‐frequency neuronavigated rTMS in auditory verbal hallucinations: a double‐blind controlled study in patients with schizophrenia. Schizophr Bull 2017. In press</ref> was identified.
  
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===Make 10-20 EEG system electrode===
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# Distance T3-Stim in the T3P3 axis are give in centimeters. "Stim" was defined as the stimulation target defined in this article <ref name="Briend 2018">Briend F. et al., Is T3P3 is the best target to treat patients suffering from schizophrenia with auditory hallucinations?. Brain Stimulation, submitted</ref>.
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Make 10-20 EEG system electrode via the Dijkstra's algorithm.
 
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* Distance T3-Stim in the T3P3 axis are give in centimeters.
 
  
 
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Revision as of 13:38, 9 March 2018

Home < Documentation < 4.8 < Modules < GeodesicSlicer


For the latest Slicer documentation, visit the read-the-docs.


GeodesicSlicer logo

Introduction and Acknowledgements

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

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

  • Dr. Olivier Etard, M.D., Ph.D., CHU de Caen.
  • 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.

Module Description

This module calculates geodesic path in 3D structure. Thanks to this geodesic path, this module could draw an EEG 10-20 system.

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 for correlating external skull locations to underlying cortical areas.[1]

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

Panels and their use

Create a mesh

Create mesh.png

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

  1. Load a volume.nii.
  2. Enter in the Geodesic Slicer module using either the toolbar or the Modules menu button.
  3. Press the button "Create a mesh".
    • Wait a moment.
  4. 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.
  5. Go to Parameters to find the shortest path or Make 10-20 EEG system electrode section.

Parameters to find the shortest path

Shortest past.png
  1. Source points: The list of fiducial points on the curve, since the "Create-and-place Fiducial" button (in green in the figure above).
  2. 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.

4 anatomical landmarks

  1. 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
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.
    • 3/the pre auricular to the left ear
    • 4/the pre auricular to the right ear
  1. Input STL model: The model you use (after "use this mesh", the t1.stl created).
  2. 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 and an anatomical target defined as the site for which stimulation was found to produce the most significant effects on AVH and was located in the left temporo-parietal cortex [2] [3] was identified.
  1. Distance T3-Stim in the T3P3 axis are give in centimeters. "Stim" was defined as the stimulation target defined in this article [4].

Information for Developers

The code is available at Github.

References

  1. ↑ Jasper, H.H. The ten-twenty electrode system of the International Federation. Electroencephalogr. Clin. Neurophysiol., 1958, 10: 370-375
  2. ↑ Hoffman RE. et al., Transcranial magnetic stimulation of Wernicke’s and Right homologous sites to curtail “voices”: a randomized trial. Biol Psychiatry 2013;73:1008–14
  3. ↑ Dollfus S. et al., Efficacy of high‐frequency neuronavigated rTMS in auditory verbal hallucinations: a double‐blind controlled study in patients with schizophrenia. Schizophr Bull 2017. In press
  4. ↑ Briend F. et al., Is T3P3 is the best target to treat patients suffering from schizophrenia with auditory hallucinations?. Brain Stimulation, submitted
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