Hello,
I am learning how to use Freesurfer command utilities and I came upon an issue. I have run a subject T1 scan through the recon-all steps and now have my parcel maps. Can someone help direct me on how I can extract individual images for each ROI label in the wmparc.mgz file? I would like to then convert these images to .nii format to read into other software for my analysis. I have performed this process with reading the .mgz into Slicer and doing it by hand(threshold image), but I assume there is a faster, less tedious way to do it using the native commands in Freesurfer. Any help or direction would be greatly appreciated.
Best, Ben -- Benjamin Pruce, R.A. Psychological and Brain Sciences Indiana University Bloomington, IN 47401