Beauchamp:RAVE:Imaging Data Formats

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Brain picture
Beauchamp Lab



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Preparing Imaging Data for RAVE

The first step for visualizing cortical surface models is to create surface models from your MRI data using FreeSurfer. See Cortical Surface models overview for more information on this step. After FreeSurfer is complete, copy the output folder into the RAVE subject folder, e.g.

 rave_data/data_dir/congruency/YAB/rave/fs

RAVE will read all of the files that are needed directly from this directory. For instance, for the left hemisphere surface model, it will read fs/surf/lh.pial.asc or (if this file is not found) it will read fs/surf/lh.pial.gii

If you only have one side of surface file, say "lh.pial.gii". You might want to create a fake "rh.pial.asc" in fs/surf/. The fake right hemisphere file contains 6 lines:

 3 1
 0 0 0
 0 0 0
 0 0 0
 0 1 2
 

The first line tells how many vertices and how many faces; line 2-4 create fake vertices at the origin; line 5 links these vertices. Please make sure the last line is blank (otherwise R will raise a warning).

To show the electrodes on the cortical surface, RAVE also needs to know the location of the implanted electrodes. See this web page for information on creating the necessary files. For more information, see Electrode Localization using iELVis (by Buffy Nesbitt)



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