Fix bounding box of labelmap after Slicer ruined it

fix_bbox.sh

# copy this script in the following directory and run from there
# cd DIAGNOSE_CTE_U01/derivatives/pnlpipe
# run as sh fix_bbox.sh

for c in $(cat incongruous_cases.txt)
do
  mask_name=sub-${c}/ses-01/dwi/sub-${c}_ses-01_desc-dwiXcCNNQc_mask.nii.gz
  bse_name=sub-${c}/ses-01/dwi/sub-${c}_ses-01_desc-dwiXc_bse.nii.gz
  
  echo $c
  
  # back up the original mask
  cp $mask_name ${mask_name}.bak
  # modify the bounding box
  antsApplyTransforms -d 3 -i $mask_name -o $mask_name -t identity -r $bse_name
  # the above step sets datatype to float64, bring it back to short/char
  fslmaths $mask_name -mul 1 $mask_name -odt char
done

  

Since the bounding box issue is coming up repetitively, I am archiving a script for fixing it.
cc @eknyazhe @sbouix