distortionCorrect

#!/bin/bash

# # # # # # # # # # # # # # # # # # 
#
# This code will use anima to do distortion
# correction of data.
#
# This code prefers to have a target directory that will
# be where derivatsive data live to keep separated
# from the orignal Subjects/ directory
#
#
#                         Robert C. Welsh
#                         Copyright 2005-2021
#
# distortionCorrection
#
# This will correct all data associated with a give task
# assuming there is a fieldMap directory in that task.
#
# Expected is:
#
#        [task]/
#            fieldMap/
#                forward.nii
#                backward.nii
#            run_01/
#                run_01.nii
#            run_02/
#                run_02.nii
#
# This script utilized anima for the correction
#
# # # # # # # # # # # # # # # # # #

#
# Main distortionCorrect function.
#

VERSION="1.0"
VERSIONDATE="2021-03-14"

# 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=" B bi f fg fi fm M MO on t U v "

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

# This is the common in-line code for the distort
. ${thisDir}/auxiliary/commonCode_Distort_01

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

# This is common code for distortion_correctionn
#. ${thisDir}/auxiliary/commonCode_Distort_02

#
# The actual function.
#

. ${thisDir}/auxiliary/parse_arguments

# Small trick to remove trailing / as needed. and remove any double-/

SUBJDIR=`dirname ${SUBJDIR}/nonsense.txt| sed -e 's/\/\//\//g'`
SUBJDIROUT=`dirname ${SUBJDIROUT}/nonsense.txt| sed -e 's/\/\//\//g'`

#

. ${thisDir}/auxiliary/superDebugStatus

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

. ${thisDir}/auxiliary/shellScriptInfo

#
# Prepare to write the script.
#

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

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

# Ok, lets do the business.

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

# Now start building the automatic scripts.

#
# the following environmental variables are from spm12Batch_Global
#
#    HOSTCOMPUTER     - name of the computer.
#    SCRIPTNAME       - name of the scripts to write.
#    UMBatchMatcher   - present working directory.
#    FULLSCRIPTNAME   - full path and name of scripts to write.
# 

# Check that all data is there to proceed.

# Now build the list of directories for each subject.

declare -i is
declare -i ii

curDIR=`pwd`

# Prepare the directory where the work is to take place.

echo "    4) checking images before building command"
echo
BAD_DATA=0
BAD_SESSIONS=

for (( is=1 ; is<=$nSubjects ; is++ ))
do
    if [ -d ${UMBatchMaster}/${SUBJDIR}/${subjects[$is]}/ ]
    then
	cd ${UMBatchMaster}/${SUBJDIR}/${subjects[$is]}/
	# Look for the field map images.
	OK_FORWARD=`ls ${fmriPATH}/${fieldMapPath}/${forwardImage} 2> /dev/null | wc -l | awk '{print $1}'`
	OK_BACKWARD=`ls ${fmriPATH}/${fieldMapPath}/${backwardImage} 2> /dev/null | wc -l | awk '{print $1}'`
	# Look for how many run images
	NRUNS=`ls ${fmriPATH}/run*/${volumeWILD}*.nii 2> /dev/null | wc -l | awk '{print $1}'`
	if [ ${NRUNS} -eq 0 ] || [ ${OK_FORWARD} -ne 1 ] || [ ${OK_BACKWARD} -ne 1 ]
	then
	    BAD_DATA=1
	    BAD_SESSION="${subjects[$is]} ${BAD_SESSIONS}"
	    echo "       Bad condition for ${subjects[$is]} runs(${NRUNS}) forward(${OK_FORWARD}) backward(${OK_BACKWARD}) "
	else
	    echo "       Good condition for ${subjects[$is]}"
	fi
    fi
done

cd ${curDIR}

if [ ${BAD_DATA} -ne 0 ]
then
    echo
    echo Found issues with the data .. prefering not to run.
    echo
    exit 1
fi

echo

. ${thisDir}/auxiliary/distortCorrect_part_01

# Common start to all shell scripts

. ${thisDir}/auxiliary/buildMatlabScripts_01

. ${thisDir}/auxiliary/shellScriptStart

#. ${thisDir}/auxiliary/distortCorrectScript


echo "    5) building shell script"
echo

# Now put in some varibles needed

. ${thisDir}/auxiliary/distortCorrect_part_02

. ${thisDir}/auxiliary/startBashSubjectLoop

# Add the distortion code to the shell script

cat ${thisDir}/auxiliary/distortCorrect_part_03 >> ${FULLSCRIPTNAME}.sh

. ${thisDir}/auxiliary/endBashSubjectLoop

# Finalize the shell script.

. ${thisDir}/auxiliary/shellScriptFinalize

# Now launch into the background if desired.

. ${thisDir}/auxiliary/shellScriptLaunch

#
# all done.
#