#!/bin/bash

# location of Morel ROIs (MNI space)
roi_dir="/mnt/c/Users/gargy/OneDrive/Desktop/morel/morel_unzipped_1mm"

#List of folders
folders=("mgh_1026" \
"mgh_1004" \
"mgh_1010" \
"mgh_1012" \
"mgh_1025" \
"mgh_1001" \
"mgh_1008" \
"mgh_1015" \
"mgh_1022" \
"mgh_1029" \
"mgh_1002" \
"mgh_1009" \
"mgh_1016" \
"mgh_1023" \
"mgh_1030" \
"mgh_1003" \
"mgh_1017" \
"mgh_1024" \
"mgh_1031" \
"mgh_1011" \
"mgh_1018" \
"mgh_1032" \
"mgh_1005" \
"mgh_1019" \
"mgh_1033" \
"mgh_1006" \
"mgh_1013" \
"mgh_1027" \
"mgh_1034" \
"mgh_1007" \
"mgh_1014" \
"mgh_1021" \
"mgh_1028")

for folder in "${folders[@]}"; do
	cd /mnt/d/HCP35/unzipped/${folder}/anat/T1/

    echo "Processing $folder"

	# Apply inverse warp to Morel ROI using nearest-neighbour interpolation
	echo "Applying the inverse warp for $folder"
	for roi in "$roi_dir"/*.nii; do
		roi_name=$(basename "$roi" .nii)
		applywarp \
			--in="$roi" \
			--ref=T1_brain.nii \
			--warp=mni2anat_warp.nii.gz \
			--out="${roi_name}_morel_native.nii.gz" \
			--interp=nn
	done
done
