
# remove outside-brain noise

for i in ../1.0.0/STAMP_*_*.nii.gz; do f=`basename $i`; fslmaths $i -mul ../1.0.0/STAMP_mask.nii.gz $f; done

# rigidly rotate to the MNI152 space
mat=mat_STAMP_rigidto_MNI152.mat
MNI152=/usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_1mm_brain.nii.gz
for i in STAMP_*_*.nii.gz; do
	dramms-warp ${i} ${mat} ${i%.nii.gz}_rigidtoMNI152.nii.gz -t ${MNI152}
done

