ENH: Script gives option to run ICV only

run_ashs_icv.sh

@@ -0,0 +1,226 @@
+#!/bin/bash -e
+
+module load c3d/20191022
+module load ashs
+
+scriptPath=$(readlink -e "$0")
+scriptDir=$(dirname "${scriptPath}")
+
+# Default atlas for 3T T1w
+icvAtlas="${ASHS_ROOT}/atlases/ICV_3TT1MRI_atlas"
+
+if [[ ! -f "${ASHS_ROOT}/bin/ashs_main.sh" ]]; then
+  echo "Cannot locate ASHS executables at ${ASHS_ROOT}/bin"
+  exit 1
+fi
+
+# Variables used in functions
+inputT1w=""
+inputT1wBasename=""
+inputT1wDirname=""
+inputT1wFileRoot=""
+outputDir=""
+
+# Submit to queue, if 1 call ashs_main with -l
+submitToQueue=0
+
+# Leave at 1 if submitting jobs, otherwise set to num procs
+greedyThreads=1
+
+# cleanup tmp dir
+cleanup=1
+
+# trim neck
+trimNeck=1
+
+##############################################
+
+function usage()
+{
+    echo "
+    $0 -g <t1w> -o <output dir> [-l <(0)|1>] [-c <(1)|0>] [-t <(1)|0>] [-I <ICV atlas>]
+    $0 -h for extended help.
+    "
+}
+
+function help()
+{
+    usage
+    echo "
+
+    This script is a simplified wrapper for ASHS ICVF estimation. See the usage for ashs_main.sh for more options.
+
+    The script requires the variable ASHS_ROOT, where \${ASHS_ROOT}/bin/ashs_main.sh exists.
+
+    Required args:
+
+      -g : Head T1w image.
+
+      -o : Output directory.
+
+
+    Options:
+
+      -c : Cleanup working directory (default = $cleanup).
+
+      -l : Parallel execution with LSF (default = $submitToQueue), for faster segmentation of a single session. If
+           processing many sessions, it's more efficient to run without this option.
+
+      -t : Trim neck from the input T1w image using the trim_neck.sh script (default = $trimNeck).
+
+
+    Custom atlas options:
+
+      -I : atlas for ICV estimation (default = $icvAtlas).
+
+      The default atlas is defined on 3T data from the Penn Memory Center. You may use custom atlases for other
+      data sets. See the ASHS website for details of atlas construction.
+
+    Referencing:
+
+    Please cite this paper when using ASHS results in published research
+
+      Yushkevich PA, Pluta J, Wang H, Ding SL, Xie L, Gertje E, Mancuso L, Kliot D, Das SR and Wolk DA,
+      \"Automated Volumetry and Regional Thickness Analysis of Hippocampal Subfields and Medial Temporal
+      Cortical Structures in Mild Cognitive Impairment\", Human Brain Mapping, 2014, 36(1), 258-287.
+      http://www.ncbi.nlm.nih.gov/pubmed/25181316
+
+    Further information:
+
+      ASHS website: https://sites.google.com/site/hipposubfields/
+    "
+}
+
+function options()
+{
+  if [[ $# -eq 0 ]]; then
+    usage
+    exit 1
+  fi
+
+  while getopts "I:c:g:l:o:t:h" opt; do
+    case $opt in
+      I) icvAtlas=$(readlink -m "$OPTARG");;
+      c) cleanup=$OPTARG;;
+      g) inputT1w=$(readlink -m "$OPTARG");;
+      l) submitToQueue=$OPTARG;;
+      o) outputDir=$(readlink -m "$OPTARG");;
+      t) trimNeck=$OPTARG;;
+      h) help; exit 1;;
+      \?) echo "Unknown option $OPTARG"; exit 2;;
+      :) echo "Option $OPTARG requires an argument"; exit 2;;
+    esac
+  done
+
+  # Check required args
+  if [[ ! -f "$inputT1w" ]]; then
+    echo "T1w image not found: $inputT1w"
+    exit 1
+  fi
+
+  inputT1wBasename=$(basename "$inputT1w")
+  inputT1wDirname=$(dirname "$inputT1w")
+
+  # Trim neck can change input, so don't allow input directory to be output directory
+  if [[ "${outputDir}" == "${inputT1wDirname}" ]]; then
+    echo "Output directory cannot be the same as the input directory"
+    exit 1
+  fi
+
+  if [[ "$inputT1wBasename" =~ .nii(.gz)?$ ]]; then
+    extension=${BASH_REMATCH[0]}
+    inputT1wFileRoot=${inputT1wBasename%${extension}}
+  else
+    echo "Input data must be in NIFTI-1 format"
+    exit 1
+  fi
+}
+
+function ICVSeg()
+{
+  queueOpt=""
+
+  if [[ $submitToQueue -eq 1 ]]; then
+    queueOpt="-l"
+  fi
+
+  ${ASHS_ROOT}/bin/ashs_main.sh \
+    -a $icvAtlas -d -T -I $inputT1wFileRoot -g $segT1w \
+    -f $segT1w \
+    -s 1-7 \
+    -B \
+    -t ${greedyThreads} \
+    -w ${jobTmpDir}/ICVSeg $queueOpt
+}
+
+function Summarize()
+{
+  cp ${jobTmpDir}/ICVSeg/final/${inputT1wFileRoot}_left_lfseg_corr_nogray.nii.gz \
+     ${outputDir}/${inputT1wFileRoot}_ICVSeg.nii.gz
+
+  cp ${jobTmpDir}/ICVSeg/final/${inputT1wFileRoot}_left_corr_nogray_volumes.txt \
+     ${outputDir}/${inputT1wFileRoot}_ICVSeg_volumes.txt
+
+  mkdir ${outputDir}/qa
+  cp -r ${jobTmpDir}/ICVSeg/qa ${outputDir}/qa/ICV_qa
+}
+
+######################################################
+
+options $@
+
+# Check we're in a bsub job
+if [[ -z "${LSB_DJOB_NUMPROC}" ]]; then
+    echo "Script must be run from within an LSB job"
+    exit 1
+fi
+
+if [[ $submitToQueue -eq 0 ]]; then
+  greedyThreads=${LSB_DJOB_NUMPROC}
+fi
+
+# Need this or NLMDenoise will attempt to use all the cores
+export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=${LSB_DJOB_NUMPROC}
+
+# make output directory
+mkdir -p ${outputDir}
+
+# Make tmp directory
+jobTmpDir=$( mktemp -d -p /scratch ashs.${LSB_JOBID}.XXXXXXX.tmpdir )
+
+if [[ ! -d "$jobTmpDir" ]]; then
+    echo "Could not create job temp dir ${jobTmpDir}"
+    exit 1
+fi
+
+# This is what gets used in the segmentation call
+segT1w=${outputDir}/${inputT1wBasename}
+
+# Optionally trim neck of input
+if [[ $trimNeck -gt 0 ]]; then
+  echo "Preprocessing: Trim neck from T1w image"
+
+  mkdir ${jobTmpDir}/neckTrim
+
+  ${scriptDir}/trim_neck.sh -d -c 10 -w ${jobTmpDir}/neckTrim $inputT1w ${segT1w}
+  echo "Preprocessing: Done!"
+else
+  cp $inputT1w ${segT1w}
+fi
+
+# perform ICV segmentation
+echo "Step 1/2: Performing intracranial volume segmentation"
+ICVSeg
+echo "Step 1/2: Done!"
+
+# reorganize and summarize the result
+echo "Step 2/2: Reorganize output and summarize the result"
+Summarize
+echo "Step 2/2: Done!"
+
+if [[ $cleanup -gt 0 ]]; then
+  rm -rf ${jobTmpDir}/ICVSeg ${jobTmpDir}/neckTrim
+  rmdir ${jobTmpDir}
+else
+  echo "Not cleaning up working directory ${jobTmpDir}"
+fi