# compute affine matrix by brain masks
for i in {1..15}; do flirt -in ../MNI152atlas/MNI152_T1_1mm_padded_brain.nii.gz -ref Template${i}_padded_str_cbq.nii.gz -omat MNI152_to_Template${i}_brain.mat

# apply the affine transform to warp with-skull images
for i in {1..15}; do flirt -in ../MNI152atlas/MNI152_T1_1mm_padded.nii.gz -ref Template${i}_padded.nii.gz -out MNI152_to_Template${i}_padded_bybrainonly.nii.gz -init MNI152_to_Template${i}_brain.mat -applyxfm & done

# apply the affine transform to warp the MNI152 FOV
for i in {1..15}; do flirt -in ../MNI152atlas/MNI152_T1_1mm_padded_FOV.nii.gz -ref Template${i}_padded.nii.gz -out Template${i}_padded_normalizedFOVmask.nii.gz -init MNI152_to_Template${i}_brain.mat -applyxfm -interp nearestneighbour & done

# apply the FOV to each template
for i in {1..15}; do fslmaths Template${i}_padded.nii.gz -mul Template${i}_padded_normalizedFOVmask.nii.gz Template${i}_padded_normalizedFOV.nii.gz & done
