Importing individual atlases in nifti format

Discussions
1

Dear Brainstormers,

We have individual resting state networks in nifti format and would like to import these into brainstorm as atlases, to be able to use them as ROIs to extract source activity. How would we do this? We tried passing an anot file using the 'load atlas' button, but we get an error saying that the number of vertices do not match.

So can actually import this then somehow into brainstorm for subjects we have already imported into brainstorm previously? If not, and we should reimport and process the subject, how would we add these resting state network maps to be picked up as atlases?

Thank you very much for your help,
Ruben

2

The simplest option is probably to work with volume head models, and import your .nii files as volume atlases.
https://neuroimage.usc.edu/brainstorm/Tutorials/TutVolSource#Volume_atlases

If you have your networks available as cortical maps (.annot) and you want to work with surface head models, then you need to re-import the anatomy with the .annot files added to the freesurfer label subfolder:
https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/io/import_anatomy_fs.m#L171

3

Hello Francois,

Thanks for the fast and useful answer.

So there is no way to transform the anot files to fit the existing surfaces?

Best,
Ruben

4

No. They need to be imported on the separated left/right high-resolution surfaces, then the hemispheres have to be merged and downsampled.
https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer#Manual_import_of_the_anatomy

If you use the same version of Matlab, you should end up with the exactly the same low-resolution surfaces, and you could probably replace the old surfaces with the new ones, or manually copy the new "atlas" from the new surface to the old one.
Therefore, if you want to keep all the work you have done, maybe you can do something like the following:

  • create a new subject,
  • import the FreeSurfer anatomy folder including the new .annot,
  • open new low-res cortex,
  • export the atlas as a scout_...mat file from the Scout tab,
  • close the figures,
  • open the old low-res cortex,
  • load the atlas.