Hi Francois,
thank you very much for your reply. I upload the atlas label file as you described above in one of your replies to Jeff, or as it was described here https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer#Manual_import_of_the_anatomy.
Apparently this application works with the annot/label files produced by Freesurfer during MR segmentation however I cannot make it work with any other atlas file outside the freesurfer segmentation folder. I attached the error message that I get if I try to upload that or any other Yeo atlas (the number of the mismatched vertices change depends on the atlas that I am trying to upload of course).
So my confusion, even though we didn't indicate the number of vertices during segmentation in freesurfer how my segmentation ended up with 134570 vertices hence it does not match the vertices of the atlas that I am trying to upload. And if I use CAT12 to run all the segmentation from the very begining, and choose 15000 vertices for the segmentation, so how come later on this segmentation could work with any Yeo atlas, whose vertices are different from 15000 vertices already but it fits somehow, but I cannot make it work manually. So does this mean, during segmentation there is a separage lh.pial files are produced for each of the default atlases anyways so they match with the annot file somehow, and since I am lacking this in my freesurfer segmentation hence I cannot upload any Yeo or Schafer atlas at all? I would really appreciate if you could give a bit more details about that please indeed. Because if I already have segmentations files are ready for all the subjects obtained with freesurfer and you know it takes ages to complete for a whole set of participants, and it would be really helpful if I can find a way to upload Yeo or Schafer atlas onto those segmentations.
Thank you very much in advance,
Kind regards
Isil
