I have individual anatomies of all participants and the FreeSurfer segmentation (conducted before I gained access to my data), and I need to get access to the Schaefer parcellations.
I'm using surface based EEG source reconstruction, so using 'Add MNI parcellation' does not work for me as it imports a volume atlas. Other than re-segmenting using CAT which is very time consuming as I have 60 subjects, is there any other way I can extract the Schaefer surface based atlas?
Thank you very much!
As it is indicated in the link shared by @Anand_Joshi, you would need to compute the cortical computations when processing the MRIs with FreeSurfer.
An non-optimal approach would be to project the desired Schaefer atlas from the Default anatomy to the Subject anatomy. This projection is based on the MNI-normalization.
-
Double-click the cortex_15002V in the Default anatomy
-
Select the desired Schaefer atlas in the Scout tab
-
Create a copy of this Atlas (because the pre-defined atlas cannot be modified)
Menu: Atlas > New atlas > Copy current atlas
-
In this new copy, select all the Scouts (Ctrl-All), then use the Menu: **Project to... > SUBJECT > CORTEX_15k **
Note: In this case, the projection happens between cortices with 15k vertices, try to do the projection between cortices of similar size
Left: Schaefer 100 parcellations, 7 networks on the Default anatomy
Right: Same atlas project to a Subject anatomy
Please note that this is only an approximation using the MNI normalization. The proper way to obtain the parcellation is during the MRI segmentation process.