Here is the code I used: ## DIR is where I put all the skull-stripped volume (output from skull-stripping function).
## of and of2 are just formatted output file names.
for f in “$DIR”/*_mri.nii.gz
/home/share/BrainSuite16a/bin/cerebro -i “$f” –atlas “/home/share/BrainSuite16a/atlas/brainsuite.icbm452.lpi.v08a.img” –atlaslabels “/home/share/BrainSuite16a/atlas/brainsuite.icbm452.v15a.label.img” -l “$DIR/$of” -o “$DIR/$of2”
For cortical_extraction.cmd: can that be executed in Linux environment? I thought it’s for windows platform. If it can, can you be a little more specific on that?