I am primarily using FSL, but open to CAT12, and with limitations to Freesurfer. I am trying to extract ventricle volumes.
After running FSL’s fast, one of the outputs are the PVE files, which are partial volume maps. However, the file pve0, corresponds to the voxels belonging to the CSF class (image below), while I need only the ventricles. Is there a way to extract the ventricle volumes with FSL?
I have experimented a bit with Freesurfer as well. However, due to limited experience, the only way I know how to extract the ventricle volumes in Freesurfer is via first completing recon-all on all NIFTI files, which takes ~2hr/NIFTI, way too long for my analysis. If someone can point me towards the minimum steps I need to do to extract the ventricle volumes, I would accept it as the answer.
CAT12 was recently recommended to me as the best tradeoff between speed and accuracy. I have 0 experience with CAT12, if anyone can point me towards an example script on how to extract the ventricle volumes I would also accept it as an answer.