I want to create binary masks in FSL based on one of the Schaefer2018 parcellations. I opened the nii.gz and corresponding lookup table in FSL. I selected only the parcels of interest from the lookup table (mPFC parcels). I expected to be able to save a binary mask based on this image.
Actual situation
I cannot figure out how to create a binary mask in FSL based on the parcels I selected. In trying to add the Schaefer atlas as an atlas in FSL, I could not because FSL requires an XML specification. And I could not find this here. How can I use the schaefer nifti file and lookup table to create an FSL atlas, so that I can create a binary mask for select regions?
rubykong
commented
1 year ago
Expected situation
I want to create binary masks in FSL based on one of the Schaefer2018 parcellations. I opened the nii.gz and corresponding lookup table in FSL. I selected only the parcels of interest from the lookup table (mPFC parcels). I expected to be able to save a binary mask based on this image.
Actual situation
I cannot figure out how to create a binary mask in FSL based on the parcels I selected. In trying to add the Schaefer atlas as an atlas in FSL, I could not because FSL requires an XML specification. And I could not find this here. How can I use the schaefer nifti file and lookup table to create an FSL atlas, so that I can create a binary mask for select regions?
Steps to reproduce the issue (optional)