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Localizing intracranial electrode locations

Page history last edited by naba.sadia.siddiqui@gmail.com 3 years, 3 months ago


The application is hosted at https://github.com/NabaSadiaSiddiqui/intracranial_electrode_localization.



  • Create grid/strip/shaft
    • Choose grid/strip/shaft name
    • Choose dimensionality
    • Choose color
  • Delete grid/strip/shaft
  • Indicate/choose grid/strip/shaft for viewing/editing
  • Indicate/advance current electrode being edited
  • Select volume trace radius for computing electrode centroid
  • Mark electrodes as missing
  • Output/import localization to file

Starting the application

  • Download or clone the project and cd into the folder MRIcroS
  • Launch the application using the command electrode.GUIController('electrodes.mat'). In case of this application, electrodes.mat is located in the examples folder. This will load up the application as follows: 


Example workflow

In this use case, we will use the application to mark 4 electrodes on the brain map.

  • [Action] In the field marked 'Name', enter a name for the grid/shaft/strip
  •  [Action] Enter the dimensions in the field labelled 'Dimensions'. In this case, we will be marking a 4x1 grid
  • [Action] Click the button 'Update Grid Dims'
  • [Observation] You will notice that the dropdown at the top will be updated with the newly created shaft
  • [Observation] The graph at the bottom will be updated with boxes to reflect the selected dimensions


The image below shows the result from performing each of the steps outlined above



  • [Action] To mark an electrode on the brain, click on a point on the brain image. The electrode will turn blue, and the corresponding position on the shaft will turn blue as well. This is show in the image below


  • [Action] To advance to the next electrode, use the right arrow key or select the electrode from the drop down list. The graph in the bottom right corner of the application shows the current grid position by shading it with "grey" color. Previously marked grid position is shaded "red". This is shown in the image below 


  • [Action] To mark the next electrode, as referenced by the newly advanced grid position, click on the point on the brain image. The previously marked electrode will turn from blue to red, and the current electrode will be blue. This is shown in the image below


  • [Observation] The image below shows the brain map after 4 iterations


  • [Action] To change the color of the marked electrodes, click on Grid Color button and pick a color. This is shown by the image below

  • [Observation] In this case, we selected yellow, and the electrodes on the brain image changed from red to yellow. This is shown in the image below 


  • [Action] To create a new grid/shaft/strip, click the Add Grid button. Note, adding a grid will automatically save the current grid/shaft/strip and all related data
  • [Action] To view all grids/shafts/strips, click on the drop down at the top of the application
  • [Action] To delete a grid, select the grid from the drop down, and click Delete Grid button.
  • [Observation] In this case, I created 2 additional grids. The image below shows the buttons/GUI elements that are used to use these features



  • [Action] To export your session to a file, click File -> Save. This will bring up a directory selector where you can specify the location to save the file to
  • [Action] To import a previous session, click File -> Load and select the input file. The application will be loaded with data from the selected *.mat file. 


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