#!/bin/bash

#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

    echo "Processing $folder"

# 0. go to directory

cd /mnt/d/HCP35/unzipped/${folder}/anat/T1/

# 1. Brain-extract the subject's T1 image first
bet T1.nii T1_brain.nii.gz -R

# 2.generate the affine matrix with flirt first:
flirt -in T1_brain.nii \
      -ref $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz \
      -omat anat2mni_affine.mat

# 3. Run FNIRT
fnirt --in=T1_brain.nii \
      --aff=anat2mni_affine.mat \
      --ref=$FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz \
      --refmask=$FSLDIR/data/standard/MNI152_T1_1mm_brain_mask_dil.nii.gz \
      --config=T1_2_MNI152_2mm \
      --cout=anat2mni_warp \
      --iout=anat2mni_fnirt.nii.gz

# 4. Invert the warp
invwarp -w anat2mni_warp.nii.gz -o mni2anat_warp.nii.gz -r T1_brain.nii

done
