final stage of struct pipeline

structure-data.sh

#!/bin/bash

run() {
  cmd="$*"
  $cmd
  if [ $? != 0 ]; then
    echo =====================
    echo $cmd 
    echo failed
    exit 1
  fi
}

usage()
{
  base=$(basename "$0")
  echo "usage: $base entries.csv results_dir release_dir
This script uploads all the results.

Arguments:
  entries.csv            Entries for the subjects (subjectID-sessionID) used for the release
  release_dir             The directory used for the release. 
  data_dir                The directory used to output the files. 
"
  exit;
}

[ $# -ge 5 ] || { usage; }

subjectID=$1
sessionID=$2
subj=$3
age=$4

releasedir=$5
datadir=`pwd`
if [ $# -ge 6 ];then 
    datadir=$6; 
fi
minimal=1
if [ $# -ge 7 ];then 
  minimal=$7
fi

action=cp
Hemi=('left' 'right');
Cortex=('CORTEX_LEFT' 'CORTEX_RIGHT');

subjdir=sub-$subjectID
sessiondir=ses-$sessionID
prefix=${subjdir}_${sessiondir}
anat=$subjdir/$sessiondir/anat
outputRawDir=$releasedir/sourcedata/$anat
outputDerivedDir=$releasedir/derivatives/$anat
outputSurfDir=$outputDerivedDir/Native
outputWarpDir=$outputDerivedDir/xfms

tmp=tmp
code_dir=~/GIT/dhcp-structural-pipeline
MNI_T1=$code_dir/atlases/MNI/MNI152_T1_1mm.nii.gz

if [ -f $outputDerivedDir/Native/${prefix}_wb.spec ]; then 
  exit
fi

run mkdir -p $outputSurfDir $outputWarpDir $outputRawDir $tmp

# raw images
run $action \
  $datadir/restore/T2/${subj}_defaced.nii.gz \
  $outputRawDir/${prefix}_T2w.nii.gz

if [ -f $datadir/T1/$subj.nii.gz ]; then
  run mirtk transform-image \
    $datadir/masks/${subj}_mask_defaced.nii.gz \
    $tmp/${subj}_mask_defaced_T1.nii.gz \
    -target $datadir/T1/$subj.nii.gz \
    -dofin $datadir/dofs/$subj-T2-T1-r.dof.gz \
    -invert

  run fslmaths \
    $datadir/T1/${subj}.nii.gz \
    -thr 0 \
    -mul $tmp/${subj}_mask_defaced_T1.nii.gz \
    $outputRawDir/${prefix}_T1w.nii.gz

  rm $tmp/${subj}_mask_defaced_T1.nii.gz
fi

# derived images
ms=T2
if [ -f $datadir/T1/$subj.nii.gz ]; then 
  ms="T1 T2"
fi

for m in ${ms}; do
  for restore in "_defaced" "_restore_defaced" "_restore_brain" "_bias"; do
    nrestore=`echo $restore |sed -e 's:_defaced::g' |sed -e 's:_bias:_biasfield:g'`
    run $action \
      $datadir/restore/$m/${subj}${restore}.nii.gz \
      $outputDerivedDir/${prefix}_${m}w${nrestore}.nii.gz
  done
done

# masks
run $action \
  $datadir/masks/$subj.nii.gz \
  $outputDerivedDir/${prefix}_brainmask_drawem.nii.gz

run $action \
  $datadir/masks/$subj-bet.nii.gz \
  $outputDerivedDir/${prefix}_brainmask_bet.nii.gz

# segmentations
for seg in all_labels tissue_labels;do
  run $action \
    $datadir/segmentations/${subj}_${seg}.nii.gz \
    $outputDerivedDir/${prefix}_drawem_${seg}.nii.gz
done

# warps
ages="$age"
if [ $age != 40 ]; then 
  ages="$ages 40"
fi

for cage in ${ages}; do
  run mirtk convert-dof \
    $datadir/dofs/template-$cage-$subj-n.dof.gz \
    $outputWarpDir/${prefix}_anat2std${cage}w.nii.gz \
    -input-format mirtk \
    -output-format fsl \
    -target $code_dir/atlases/non-rigid-v2/T2/template-$cage.nii.gz \
    -source $outputRawDir/${prefix}_T2w.nii.gz

  run mirtk convert-dof \
    $datadir/dofs/$subj-template-$cage-n.dof.gz \
    $outputWarpDir/${prefix}_std${cage}w2anat.nii.gz \
    -input-format mirtk \
    -output-format fsl \
    -source $code_dir/atlases/non-rigid-v2/T2/template-$cage.nii.gz \
    -target $outputRawDir/${prefix}_T2w.nii.gz
done

# surfaces, which might be missing ... look for MyelinMap, since that will
# only be made at the end of surface extraction
surfdir=$datadir/surfaces/$subj/workbench
if [ -f $surfdir/$subj.L.SmoothedMyelinMap.native.func.gii ]; then
  for f in corrThickness curvature drawem inflated pial roi sphere sulc thickness white MyelinMap; do
    sfiles=`ls $surfdir/$subj.*$f*`
    for sf in ${sfiles}; do
      so=`echo $sf | sed -e "s:$surfdir.::g"|sed -e "s:$subj.:${prefix}_:g"`
      # bids:
      so=`echo $so | sed -e 's:corrThickness:corr_thickness:g' | sed -e 's:SmoothedMyelinMap:smoothed_myelin_map:g' | sed -e 's:MyelinMap:myelin_map:g'`
      so=`echo $so | sed -e 's:.native::g' | sed -e 's:_L.:_left_:g'| sed -e 's:_R.:_right_:g'`
      
      run $action $sf $outputDerivedDir/Native/$so
    done
  done

  wbvols="T2w_restore"
  wbmetrics="sulc thickness curvature corr_thickness"
  wbsurfs="white pial midthickness inflated very_inflated sphere"

  if [ -f $datadir/T1/$subj.nii.gz ]; then
    wbvols="$wbvols T1w_restore T1wdividedbyT2w T1wdividedbyT2w_ribbon"
    wbmetrics="$wbmetrics myelin_map smoothed_myelin_map"
    # myelin images etc.
    run $action \
      $surfdir/$subj.ribbon.nii.gz \
      $outputDerivedDir/${prefix}_ribbon.nii.gz

    run $action \
      $surfdir/$subj.T1wDividedByT2w_defaced.nii.gz \
      $outputDerivedDir/${prefix}_T1wdividedbyT2w.nii.gz

    run $action \
      $surfdir/$subj.T1wDividedByT2w_ribbon.nii.gz \
      $outputDerivedDir/${prefix}_T1wdividedbyT2w_ribbon.nii.gz
  fi

fi

if [ ! $minimal -eq 1 ]; then
  # segmentations
  seg=labels
  run $action \
    $datadir/segmentations/${subj}_${seg}.nii.gz \
    $outputDerivedDir/${prefix}_drawem_${seg}.nii.gz
  
  # warps
  for cage in ${ages}; do
    run mirtk convert-dof \
      $datadir/dofs/template-$cage-$subj-n.dof.gz \
      $tmp/template-$cage-$subj-r.dof.gz \
      -input-format mirtk \
      -output-format rigid

    run mirtk convert-dof \
      $datadir/dofs/$subj-template-$cage-n.dof.gz \
      $tmp/$subj-template-$cage-r.dof.gz \
      -input-format mirtk \
      -output-format rigid

    run mirtk convert-dof \
      $tmp/template-$cage-$subj-r.dof.gz \
      $outputWarpDir/${prefix}_anat2std${cage}w.mat \
      -input-format mirtk \
      -output-format fsl \
      -target $code_dir/atlases/non-rigid-v2/T2/template-$cage.nii.gz \
      -source $outputRawDir/${prefix}_T2w.nii.gz

    run mirtk convert-dof \
      $tmp/$subj-template-$cage-r.dof.gz \
      $outputWarpDir/${prefix}_std${cage}w2anat.mat \
      -input-format mirtk \
      -output-format fsl \
      -source $code_dir/atlases/non-rigid-v2/T2/template-$cage.nii.gz \
      -target $outputRawDir/${prefix}_T2w.nii.gz

    run $action \
      $tmp/template-$cage-$subj-r.dof.gz \
      $outputWarpDir/${prefix}_anat2std${cage}w-r.dof.gz

    run $action \
      $tmp/$subj-template-$cage-r.dof.gz \
      $outputWarpDir/${prefix}_std${cage}w2anat-r.dof.gz

    run $action \
      $datadir/dofs/template-$cage-$subj-n.dof.gz \
      $outputWarpDir/${prefix}_anat2std${cage}w-n.dof.gz

    run $action \
      $datadir/dofs/$subj-template-$cage-n.dof.gz \
      $outputWarpDir/${prefix}_std${cage}w2anat-n.dof.gz

  done

  if [ -f $datadir/dofs/$subj-MNI-n.dof.gz ]; then 
    run mirtk convert-dof \
      $datadir/dofs/$subj-MNI-n.dof.gz \
      $tmp/$subj-MNI-r.dof.gz \
      -input-format mirtk \
      -output-format rigid

    run mirtk convert-dof \
      $datadir/dofs/$subj-MNI-n.dof.gz \
      $outputWarpDir/${prefix}_MNI2anat.nii.gz \
      -input-format mirtk \
      -output-format fsl \
      -target $outputRawDir/${prefix}_T2w.nii.gz \
      -source $MNI_T1

    run mirtk convert-dof \
      $datadir/dofs/$subj-MNI-r.dof.gz \
      $outputWarpDir/${prefix}_MNI2anat.mat \
      -input-format mirtk \
      -output-format fsl \
      -target $outputRawDir/${prefix}_T2w.nii.gz \
      -source $MNI_T1

    run $action \
      $datadir/dofs/$subj-MNI-n.dof.gz \
      $outputWarpDir/${prefix}_MNI2anat-n.dof.gz

    run $action \
      $tmp/$subj-MNI-r.dof.gz \
      $outputWarpDir/${prefix}_MNI2anat-r.dof.gz
  fi

  if [ -f $datadir/T1/$subj.nii.gz ]; then
    run $action \
      $datadir/dofs/$subj-T2-T1-r.mat \
      $outputWarpDir/${prefix}_T1w2anat.mat

    run $action \
      $datadir/dofs/$subj-T2-T1-r.dof.gz \
      $outputWarpDir/${prefix}_T1w2anat-r.dof.gz
  fi

  # copy posteriors
  outputPostDir=$outputDerivedDir/posteriors
  mkdir -p $outputPostDir
  structs=`ls $datadir/posteriors`
  for str in ${structs}; do
    run $action \
      $datadir/posteriors/$str/$subj.nii.gz \
      $outputPostDir/${prefix}_drawem_${str}.nii.gz
  done

fi

# don't make the spec files -- too annoying
exit 

# create spec file
cd $outputDerivedDir/Native

spec=${prefix}_wb.spec
rm -f $spec

for hi in {0..1}; do
  h=${Hemi[$hi]}
  C=${Cortex[$hi]}
  for surf in ${wbsurfs};do
    run wb_command -add-to-spec-file $spec $C ${prefix}_${h}_$surf.surf.gii
  done
done

C=INVALID
for metric in ${wbmetrics};do
    run wb_command -add-to-spec-file $spec $C ${prefix}_$metric.dscalar.nii
done
run wb_command -add-to-spec-file $spec $C ${prefix}_drawem.dlabel.nii

for file in ${wbvols};do
  run wb_command -add-to-spec-file $spec $C ../${prefix}_$file.nii.gz
done