RAVE:LocalizeElectrodes

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Localize Electrodes

RAVE reads the file electrodes.csv to store information about each electrode, one row per electrode. Because electrode locations are different in every subject, each subject has a different electrodes.csv file, located in the directory tree

 proj_name/subj_name/rave/meta/electrodes.csv 

Here is the contents of a sample electrodes.csv file:

   Electrode   Coord_x     Coord_y   Coord_z    Label
       13      -68.86721   7.1108970 15.57871   G13
       14      -70.83457  -0.7146498 17.87189   G14
       15      -71.80737  -9.9609583 22.41152   G15

There are five required columns in each electrodes.csv file. The first column must be labelled "Electrode" and lists a unique number for each electrode (typically, the clinical channel number used to record data from that electrode). The second column must be labelled "Coord_x" and contains the x-coordinate of the electrode in the tk-RAS (FreeSurfer) coordinate system. The third column and fourth columns are the y and z co-ordinates. The fifth column must be called "Label" and contains the name of electrode. Additional columns may also be present in the file. For instance, the cortical surface vertex closest to the electrode; the anatomical location of the electrode; and so on. If there are additional columns, RAVE will read them and allow you to filter electrodes accordingly (e.g. "only electrodes with label = superior temporal").

There are many solutions for localizing electrodes. For more information, see

  1. Beauchamp:Electrode Localization and Naming
  2. Creating a Surface Model and Electrode Localization (by Muge Ozker Sertel)
  3. Electrode Localization using iELVis (by Buffy Nesbitt)
  4. Electrode Localization using steps from the ALICE package
  5. Electrode Localization using steps from the img_pipe package

RAVE contains experimental tools for electrode localization, access with

 rave::rave_preprocess(beta=TRUE)


Automatic Label Generation

RAVE provides tools to generate additional electrode labels automatically if FreeSurfer or SUMA files are provided. The following script calculates MNI305 coordinates and nearest hemisphere etc. Simply replace `project_name` and `subject_code` before executing.

project_name <- "demo"
subject_code <- "YAB"
brain <- rave::rave_brain2(sprintf('%s/%s', project_name, subject_code))
brain$electrodes$raw_table$SurfaceElectrode <- TRUE
tbl <- brain$calculate_template_coordinates()
rave::save_meta(data = tbl, meta_type = 'electrodes', project_name, subject_code)

The fully expanded electrodes.csv with optional columns looks like this.

Electrode   Coord_x     Coord_y  Coord_z    Label  MNI305_x  MNI305_y  MNI305_z SurfaceElectrode      SurfaceType Radius VertexNumber Hemisphere
13         -68.86721   7.1108970 15.57871   G13    -75.58190 -11.96114 -7.205155 TRUE                  pial         2       139280       left
14         -70.83457  -0.7146498 17.87189   G14    -77.13832 -21.71118 -2.563521 TRUE                  pial         2       144135       left
15         -71.80737  -9.9609583 22.41152   G15    -77.52183 -33.03184  5.295971 TRUE                  pial         2       144936       left
     

Columns MNI305_x, MNI305_y, MNI305_z are MNI305 coordinates. Column SurfaceElectrode is logical TRUE/FALSE indicating whether the electrode is grid electrode floating on the surface (TRUE) or depth electrode inserted (FALSE). Column SurfaceType is for surface electrodes only, indicating the nearest surface structure. Column Radius will affect electrode render sizes. Column Hemisphere is the nearest hemisphere (left/right). If SUMA standard 141 brain is used, column VertexNumber will be the vertex number of corresponding hemisphere that is closest to the electrode. If SUMA standard 141 brain is missing, or the electrode is marked as depth electrode, VertexNumber will be -1.




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