melanin_align

#!/usr/bin/env bash
set -euo pipefail

# @param NMinput - xxxx_NM.nii.gz file
# @param T1DIR - dir containing: 'mprage_warpcoef.nii.gz', 'mprage_bet_fast_wmseg.nii.gz'
# @output - neuromelanin aligned atlases (in CWD) 
#
# depends on preprocessMprage, assumes 2mm template used (atlases match 2mm mni2009c)

# 20200909WF - update with VTASNLC, fix SN 2mm, fix NN->NM typo, add doc, add log

[ $# -ne 2 ] && echo "USAGE: $0 NM.nii.gz T1ProcDir" && exit 1
orgiargs="$@"
input="$1"; shift
T1DIR="$1"; shift
test ! -r $T1DIR/mprage_bet.nii.gz && echo "bad t1 preproc dir, bet file DNE: '$_'!" && exit 1
test ! -r $T1DIR/mprage_warpcoef.nii.gz && echo "bad t1 preproc dir, warp file DNE: '$_'!" && exit 1
[ ! -r $input ] && echo "bad input '$input' (pwd: $PWD)!" && exit 1
! [[ $input =~ .nii.gz$ ]] && echo "neuromelanin input must end with nii.gz ('$input')" && exit 1
in=$(basename $input .nii.gz)

[[ $in =~ NN$ ]] && echo "ERROR: expect input '$input' to end in NN.nii.gz" && exit 1

set -x
# link in mprage
! test -r t1-bet.nii.gz &&
  ln -s $T1DIR/mprage_bet.nii.gz $_

# 20200909 - this always runs. never changes `-orient` value (always "RPI")
# # reorient to match t1-bet, probably "RPI"
# [ ! -r $in.nii.gz -o $(3dinfo -orient $in.nii.gz ) != $(3dinfo -orient t1-bet.nii.gz) ] &&
#   niinote $input \
#     fslreorient2std $input $in.nii.gz

! test -r $in-bet.nii.gz &&
  niinote $_ \
   bet $in.nii.gz $_  -f .01

! test -r ${in}_t1.nii.gz &&
   niinote $_ \
    flirt -dof 6 -in $in-bet.nii.gz -ref  t1-bet.nii.gz  -omat $in-T1.mat -out $_

if [ ! -r T12NM.mat ]; then
   cat $in-T1.mat
   convert_xfm -omat T12NM.mat -inverse $in-T1.mat
fi

# warp others to nn
name=${in%%-NM}

! test -r ${name}-fastwm_NM.nii.gz &&
  niinote $_ \
    flirt -interp nearestneighbour -in $T1DIR/mprage_bet_fast_wmseg.nii.gz -ref $in.nii.gz -applyxfm -init T12NM.mat -out $_

# 20200909 - to inspect warp put t1 in NM space
! test -r t1-bet_NM.nii.gz &&
  niinote $_ \
    flirt -in t1-bet.nii.gz -out $_ -ref $in -applyxfm -init T12NM.mat

! test -r mni2t1.nii.gz &&
  niinote $_ \
   invwarp -w $T1DIR/mprage_warpcoef.nii.gz -r t1-bet.nii.gz -o $_ 

! test -r ${name}-mnigm_NM.nii.gz &&
  niinote $_ \
   applywarp \
    -i /opt/ni_tools/standard_templates/mni_icbm152_nlin_asym_09c/mni_icbm152_wm_tal_nlin_asym_09c_2mm.nii  \
    -w mni2t1.nii.gz \
    --postmat=T12NM.mat \
    -r $in.nii.gz \
    -o $_

! test -r $name-CC_NM.nii.gz &&
  niinote $_ \
    applywarp \
      --interp=nn \
      -i /opt/ni_tools/atlas/CC/nm_CC_mask_2mm.nii.gz \
      -w mni2t1.nii.gz \
      --postmat=T12NM.mat \
      -r $in.nii.gz \
      -o $_

! test -r $name-SN_NM.nii.gz &&
  niinote $_ \
    applywarp \
      --interp=nn \
      -i /opt/ni_tools/atlas/CC/nm_SN_mask_2mm.nii.gz \
      -w mni2t1.nii.gz \
      --postmat=T12NM.mat \
      -r $in.nii.gz \
      -o $_

! test -r $name-VTASNLC_NM.nii.gz &&
  niinote $_ \
    applywarp \
      --interp=nn \
      -i /opt/ni_tools/atlas/CC/VTASNLC_up2mm.nii.gz \
      -w mni2t1.nii.gz \
      --postmat=T12NM.mat \
      -r $in.nii.gz \
      -o $_

! test -r ${in}_mni.nii.gz && 
  niinote $_ \
   applywarp \
    -i $in.nii.gz \
    -w $T1DIR/mprage_warpcoef.nii.gz \
    --premat=$in-T1.mat \
    -r /opt/ni_tools/standard_templates/mni_icbm152_nlin_asym_09c/mni_icbm152_t1_tal_nlin_asym_09c_2mm.nii \
    -o $_ &&
  3dNotes -h "$0 $orgiargs" $_

# log if we made any new files
[ $(find . -type f -mtime -1 |sed 1q | wc -l) -gt 0 ] &&
   echo "$0 $orgiargs # ver $(gitver $0) @ $(date)" >> nm_log.txt || :