erodeMask

#!/bin/bash

# # # # # # # # # # # # # # # # # # 
#
# A command to erode the p2 and p3 segments from VBM8
# of the c2 and c3 segments from newSeg
# in a directory and turn into WMMask and CSFMask
#
#
#   p2 is WM
#   p3 is CSF
#
#   c2 is WM
#   c2 is CSF
#
#
#                         Robert C. Welsh
#                         Copyright 2005-2011
#
# erodeMask
#
# This command always runs in the foreground
# as it won't write a script file.
#
# # # # # # # # # # # # # # # # # #

#
# Main erodeMask function.
#

VERSION="1.1"
VERSIONDATE="2012-12-21"

# Find out where the current command lives and execute some common code.

theFullCommand="$0 $*"
execDIR=`pwd`

# Find out where the current command lives and execute some common code.

theCommand=`which $0`
thisDir=`dirname $theCommand`

thisCommand=`echo $theCommand | awk -F/ '{print $NF}'`

allowedOptions=" D d E h M L m on v w "

# This piece of code all of the spm12Batch scripts will use
. ${thisDir}/auxiliary/commonCode_AllScriptsStart

# Validate that we have FSL installed.
. ${thisDir}/auxiliary/commonCode_FSL_01

# This is common in-line code for all spm12Batch script to make sure arguments were passed
. ${thisDir}/auxiliary/commonCode_checkIfArgsPassed

#
# The actual function.
#

. ${thisDir}/auxiliary/parse_arguments

#

. ${thisDir}/auxiliary/superDebugStatus

#
# Ok - let's start displaying things back to the terminal
#

. ${thisDir}/auxiliary/shellScriptInfo

#
# Prepare to write the script.
#

# Makes sure they speficied some subjects.
. ${thisDir}/auxiliary/checkInputForSubjects

# Write out debug status
. ${thisDir}/auxiliary/debugStatus

# Print out the list of subjects that we operate upon.
. ${thisDir}/auxiliary/printSubjectsList

# Make two loops, one to check that images p2 and p3 exist for all subjects, if they don't we will
# bugger out.

BAD=0

# Set the erosion options

WMEROSION_FACTOR=
CSFEROSION_FACTOR=
for iErosion in `seq 1 1 ${WMEROSION}`
do
    WMEROSION_FACTOR="${WMEROSION_FACTOR} -ero"
done

for iErosion in `seq 1 1 ${CSFEROSION}`
do
    CSFEROSION_FACTOR="${CSFEROSION_FACTOR} -ero"
done

echo
echo "WM erosion factor  : ${WMEROSION_FACTOR}"
echo
echo "CSF erosion factor : ${CSFEROSION_FACTOR}"
echo

# Now determine the name of the images we are looking for to do the erosion

if [ "${EROSIONLAST}" == 1 ]
then
    echo "Eroding the final segments."
    WMSEG=${volumeWILD}p2${HIRESNAME}
    CSFSEG=${volumeWILD}p3${HIRESNAME}
    WMSEGALT=${volumeWILD}c2${HIRESNAME}
    CSFSEGALT=${volumeWILD}c3${HIRESNAME}
else
    echo "Eroding the intermediate segments."
    WMSEG=wrp2${HIRESNAME}
    CSFSEG=wrp3${HIRESNAME}
fi

for WORK in 0 1
do  
    for (( is=1 ; is<=$nSubjects ; is++ ))
    do
	SUBJECTANATOMY=${UMBatchMaster}/${SUBJDIR}/${subjects[$is]}/${coregPATH}
	if [ ! -d "${SUBJECTANATOMY}" ]
	then
	    echo
	    echo "   FATAL ERROR, can't find directory ${SUBJECTANATOMY}"
	    echo
	    echo
	    exit 0
	fi
	cd ${SUBJECTANATOMY}
	# 
	# Count the number present.
	#
	nP2PRESENT=`ls ${WMSEG}*.nii 2> /dev/null | wc -l `
	nP3PRESENT=`ls ${CSFSEG}*.nii 2> /dev/null | wc -l `
	if [ ${nP2PRESENT} -ne 1 ] 
	then
	    nP2PRESENT=`ls ${WMSEGALT}*.nii 2> /dev/null | wc -l`
	    if [ ${nP2PRESENT} -ne 1 ] 
	    then
		BAD=1
	    else
		WMSEG=${WMSEGALT}
	    fi
	fi
	if [ ${nP3PRESENT} -ne 1 ] 
	then
	    nP3PRESENT=`ls ${CSFSEGALT}*.nii 2> /dev/null | wc -l`
	    if [ ${nP3PRESENT} -ne 1 ] 
	    then
		BAD=1
	    else
		CSFSEG=${CSFSEGALT}
	    fi
	fi
	if [ ${BAD} == 1 ] 
	then
	    echo
	    echo Can not find proper segments for ${SUBJECTANATOMY}
	    echo
	fi
	if [ "${WORK}" == 1 ] 
	    then
	    echo Working on subject ${subjects[$is]}
	    # 
	    # erode the WM first
	    #
	    FILENAME=`ls ${WMSEG}* | awk -F.nii '{print $1}'`
            echo "    WM ${FILENAME}"
	    fslmaths ${FILENAME} ${mcOPT} -bin ${WMEROSION_FACTOR} WM_${outputName}${FILENAME}
	    logTheUMProcess erodeMask erodeMask ${FILENAME} "-> ${mcOPT} ${WMEROSION_FACTOR} ->" WM_${outputName}${FILENAME}
	    if [ "${EROSIONLAST}" == 0 ]
	    then
		. ${thisDir}/auxiliary/resampleSegSpace WM_${outputName}${FILENAME} WM_${outputName}${volumeWILD}${FILENAME} wrp2${HIRESNAME} ${volumeWILD}p2${HIRESNAME} 
		logTheUMProcess erodeMask erodeMask WM_${outputName}${FILENAME} "Using  wrp2${HIRESNAME} -> ${volumeWILD}p2${HIRESNAME}" WM_${outputName}${volumeWILD}${FILENAME}
	    fi
	    #
	    # Now the CSF
	    #
	    FILENAME=`ls ${CSFSEG}* | awk -F.nii '{print $1}'`
            echo "    CSF ${FILENAME}"
	    fslmaths ${FILENAME} ${mcOPT} -bin ${CSFEROSION_FACTOR} CSF_${outputName}${FILENAME}
	    logTheUMProcess erodeMask erodeMask ${FILENAME} "-> ${mcOPT} ${CSFEROSION_FACTOR} ->" CSF_${outputName}${FILENAME}
	    if [ "${EROSIONLAST}" == 0 ]
	    then
		. ${thisDir}/auxiliary/resampleSegSpace CSF_${outputName}${FILENAME} CSF_${outputName}${volumeWILD}${FILENAME} wrp3${HIRESNAME} ${volumeWILD}p3${HIRESNAME}
		logTheUMProcess erodeMask erodeMask CSF_${outputName}${FILENAME} "Using  wrp3${HIRESNAME} -> ${volumeWILD}p3${HIRESNAME}" CSF_${outputName}${volumeWILD}${FILENAME}
	    fi
	    #
	    echo
	fi
	cd ${thisDir}
    done
done

#
# All done.
#