Takes freesurfer label files and creates MNI 2mm volumes. Set for left hemisphere labels.

volumes_from_labels.sh

#!/bin/bash
# execute one directory above labeldir and volumedir
# usage: ./volumes_from_labels.sh

volumedir='volumedir'
if [ ! -d $volumedir ]; then
    mkdir volumedir
fi
    
for lab in `ls labeldir/l*.label`; do
    name=`echo $lab | cut -d "." -f 1 | cut -d "/" -f 2`
    mri_label2vol --label $lab --temp $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --o ${volumedir}/${name}.nii.gz --proj frac 0 1 0.01 --subject fsaverage --hemi lh
done