###############################
# step 1. padding images and label images (inferior and superior)

for i in {1..15}; do
	3dZeropad -I 15 -S 15 -A 15 -P 15 -L 15 -R 15 -prefix Template${i}_padded.nii.gz Template${i}.nii.gz
	3dZeropad -I 15 -S 15 -A 15 -P 15 -L 15 -R 15 -prefix Template${i}_padded_label.nii.gz Template${i}_str_cbq.nii.gz
done



# check before removign
for i in {1..15}; do
	\rm Template${i}.nii.gz Template${i}_str_cbq.nii.gz
done


##############################
# step2. check if any image has negative values

# found Template11, then assigned intensity 0 to those voxels
fslmaths Template11_padded.nii.gz -bin -mul Template11_padded.nii.gz haha.nii.gz
mv haha.nii.gz Template11_padded.nii.gz


##############################
# step 3. normalize FOV by registering brain masks, not the brain image from MNI152

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

# 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



