Import custom ROIs (*.label files) in Brainstorm

Requests
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1

Hi Francois,

We are working on a project that requires custom fMRI-defined ROIs (*.label files from Freesurfer). Unfortunately Brainstorm does not support an efficient way to import the original label files because the imported surfaces change due to downsampling. Would it be possible to have an effective way to:
i) Add new ROIs after the Freesurfer folder has already been imported.
ii) Add new ROIs while running 'Import anatomy folder'

A possible approach for (i) is to store the mapping from the high to the low resolution surface and apply it to the new high-resolution *.label files. A possible approach for (ii) is to allow the user to create an additional folder in the Freesurfer folder (e.g. /label/user_labels/) and automatically import these during 'import anatomy folder'. Either solution would be great, or whatever you think appropriate. The advantages of (i) are that you can add labels at any time in your project, and that it does not add custom folders in the Freesurfer structure. But (ii) is also great.

Currently, we are following a very convoluted approach to proceed with our project involving these steps:

  1. import freesurfer anatomy folder, which automatically generates the downsampled cortical surface used in the source localization procedure.
  2. delete this downsampled cortical surface file so that it is replaced properly by the one I create later
  3. since they are deleted after being used to create the downsampled surface mentioned above, I manually re-import the rh and lh pial surface files from the surf/ subfolder of the freesurfer anatomy folder
  4. on these surfaces individually, the .label files created for reach fROI can be added to the "User Atlas" of scouts
  5. merge the rh and lh pial surfaces -- creates a full surface of original size
  6. downsample to 15000 vertices -- this creates a file named appropriately to be used (as a replacement for the one deleted in step 2) in the source localization procedure without any further steps to specify it -- it automatically selects this file downstream

Thank you,
Dimitrios & Kirsten

2

Hi Dimitrios,

I modified the FreeSurfer reader to import ALL the .annot files in the /label folder.
You only have to add your .annot files in there and import the FreeSurfer subject folder with the menu "Import anatomy folder".
https://github.com/brainstorm-tools/brainstorm3/commit/90ef13e959d024234830e98677c83fc7cca131cc

Importing additional .annot files when the anatomy folder is already imported is a lot more complicated, because the information needed for reading the parcellation is deleted at that stage.
If this is really what you need, it would be better to write a script specific for your study, since this will never be of a standard way of handling FreeSurfer data in Brainstorm.
Do you need help with this?

Francois