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!
Please check this tutorial:
https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer#Cortical_parcellations
The Schaefer atlas is included. thanks,
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.
Thank you for the reply!
A couple of follow up questions:
I attempted a manual mapping between the 'Schaefer_100_17net' from CAT segmentation, and 'Schaefer_100_7net' from the MNI approximation. However, there are some discrepancies in the regions.
CAT12 MRI segmentation does provided an MRI volume segmented with the 7 networks. You can use CAT12 segmentation instead of FreeSurfer segmentation, but you need to perform MRI segmentation again.
Indeed they are, CAT12 does not only uses a linear transformation to label voxels in the Schaefer networks. This is what it was shown in my previous post, and that is why it was mentioned that projecting the Schaefer atlases from the Default anatomy and projected was a non-optimal approach.
Because am cortical parcellation is not functional data. There is no way to show it in the Functional data view. Please check in detail the Scout tutorial to see how to use scout atlases (sets if Scouts):
