motionScrub.sh

#!/bin/bash

##################################################################################################################
# Motion Scrubbing (Censoring TRs with too much movement (Power 2012 Neuroimage)
#     1. Scrubbing
#       a. 0=No Scrubbing
#       b. 1=Motion Scrubbing
#       c. 2=No Scrubbing, Motion Scrubbing in parallel
##################################################################################################################

scriptPath=$(perl -e 'use Cwd "abs_path";print abs_path(shift)' "$0")
scriptDir=$(dirname "$scriptPath")
filename=run_motionscrub.m


function Usage {
  echo "Usage: motionScrub.sh -f restingStateImage"
  echo " where"
  echo "  -E resting state image"
  echo "    *Top-level RestingState.nii.gz image"
  echo "  -h help"
  exit 1
}

########## FSL's arg parsing functions ###################
get_opt1() {
    arg=${1//=*/}
    echo "$arg"
}


get_imarg1() {
    arg=$(get_arg1 "$1");
    arg=$("$FSLDIR"/bin/remove_ext "$arg");
    echo "$arg"
}

get_arg1() {
    if [ X"$(echo "$1" | grep '=')" = X ] ; then
	echo "Option $1 requires an argument" 1>&2
	exit 1
    else
	arg=${1//*=/}
	if [ X"$arg" = X ] ; then
	    echo "Option $1 requires an argument" 1>&2
	    exit 1
	fi
	echo "$arg"
    fi
}


# Parse Command line arguments
if [ $# -lt 1 ] ; then Usage; exit 0; fi
while [ $# -ge 1 ] ; do
    iarg=$(get_opt1 "$1");
    case "$iarg"
	in
    --epi)
  	    epiData=$(get_arg1 "$1");
        export epiData;
        indir=$(dirname "$epiData");
        export indir;
        rawEpiDir=$(dirname "$(x=$indir; while [ "$x" != "/" ] ; do x=$(dirname "$x"); find "$x" -maxdepth 1 -type f -name "mcImg.nii.gz"; done 2>/dev/null)");
        export rawEpiDir
        if [ "$epiData" == "" ]; then
          echo "Error: The restingStateImage (-E) is a required option"
          exit 1
        fi
  	    shift;;
    -h)
      Usage;
      exit 0;;
    *)
      echo "Unrecognised option $1" 1>&2
      exit 1
     esac
done


##Echo out all input parameters into a log
logDir=$rawEpiDir
{ 
  echo "$scriptPath"
  echo "------------------------------------"
  echo "-E $epiData"
  date
  echo ""
  echo ""
} >> "$logDir"/rsParams_log

cd "$indir" || exit
gunzip "${epiData}"


echo "Running $0 ..."



cd "$rawEpiDir" || exit


# Extract image dimensions from the NIFTI File
numXdim=$(fslinfo "$epiData" | grep ^dim1 | awk '{print $2}')
numYdim=$(fslinfo "$epiData" | grep ^dim2 | awk '{print $2}')
numZdim=$(fslinfo "$epiData" | grep ^dim3 | awk '{print $2}')
numtimepoint=$(fslinfo "$epiData" | grep ^dim4 | awk '{print $2}')


 

#### Motion scrubbing ############

echo "...Scrubbing data"
cat > $filename << EOF
% It is matlab script
addpath('${scriptDir}')
niftiScripts=['${scriptDir}','/Octave/nifti'];
addpath(niftiScripts)
funcvoldim=[${numXdim} ${numYdim} ${numZdim} ${numtimepoint}];
motionscrub('${rawEpiDir}','${epiData//.nii.gz/.nii}',funcvoldim)
quit
EOF



# Run script using Matlab or Octave
haveMatlab=$(which matlab)
if [ "$haveMatlab" == "" ]; then
  octave --no-window-system "$rawEpiDir/$filename"
else
  matlab -nodisplay -r "run $rawEpiDir/$filename"
fi

#################################


cd "${rawEpiDir}"/motionScrub || exit
#### Process Summary ############
echo "...Summarizing Results"

##Want to summarize motion-scrubbing output
echo "ID,total_volumes,deleted_volumes,prop_deleted,resid_vols" > motion_scrubbing_info.txt

fsl_tsplot -i fd.txt -t "FD (mm)" -w 800 -h 300 -u 1 --start=1 -o fd.png
fsl_tsplot -i dvars.txt -t "DVARS" -w 800 -h 300 -u 1 --start=1 -o dvars.png
##Echo out the pertinent info for the motion-scrubbed/processed subjects

numvols=$(fslinfo "${epiData}" | grep ^dim4 | awk '{print $2}')

delvols=$(wc < deleted_vols.txt | awk '{print $2}')

propdel=$(echo "${numvols} ${delvols}" | awk '{print ($2/$1)}')
residvols=$(echo "${numvols} ${delvols}" | awk '{print ($1-$2)}')
echo "${indir},${numvols},${delvols},${propdel},${residvols}" >> motion_scrubbing_info.txt

#Echo out motionscrub info to rsParams file
echo "epiNormMS=${epiData//.nii/_ms.nii}" >> "$rawEpiDir"/rsParams


{
  echo "<hr>"
  echo "<h2>Motion Scrubbing</h2>"
  echo "<b>Total Volumes</b>: $numvols<br>"
  echo "<b>Deleted Volumes</b>: $delvols<br>"
  echo "<b>Remaining Volumes</b>: $residvols<br>"
 } >> "${rawEpiDir}"/analysisResults.html


scrubDataCheck=$(head -1 deleted_vols.txt)
if [[ $scrubDataCheck != "" ]]; then
  echo "<b>Scrubbed TR</b>: $(awk '{$1=$1}1' deleted_vols.txt)<br>" >> "${rawEpiDir}"/analysisResults.html
fi

#################################
# clean up gunzipped nifti
gzip "${epiData//.nii.gz/.nii}"

echo "$0 Complete"
echo ""
echo ""