coregHiRes

#!/bin/bash

# # # # # # # # # # # # # # # # # # 
#
# A command to make it easier on the user to coregister the 
# HiRes to the overlay image.. 
#
# This command will build a script to run and will also 
# run the script in background.
#
#   e.g.    coregHiRes
#
#
#                         Robert C. Welsh
#                         Copyright 2005-2011
#
# coregHiRes
#
# SPM12 Version, only works with NIFTI and NIFTI_GZ, but not NIFTI_PAIR
#
# # # # # # # # # # # # # # # # # #

#
# Main coregHiRes function.
#

VERSION="2.1"
VERSIONDATE="2011-07-29"

# 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="aDdfhMnOoRrtUw"  - "reslice only" is NOT working with other images.
allowedOptions=" a B D d f h M on O o r r t U w "

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

# This is common in-line code for the coregistration steps.
. ${thisDir}/auxiliary/commonCode_CoReg_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

# Ok, lets do the business.

# Write out the status of the reslicing flag.
. ${thisDir}/auxiliary/coregResliceStatusMsg

# 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.
#    MATLABDIR        - location of the scripts.
#    UMBatchMatcher   - present working directory.
#    FULLSCRIPTNAME   - full path and name of scripts to write.
# 

. ${thisDir}/auxiliary/coregPart_01

# Now build the list of directories for each subject.

echo "UMImgPairs    = {..."                               >> ${FULLSCRIPTNAME}.m

declare -i is
declare -i ii

curDIR=`pwd`

for (( is=1 ; is<=$nSubjects ; is++ ))
do
    cd ${UMBatchMaster}/${SUBJDIR}/${subjects[$is]}/

  #
  # check the coregistation directory.
  #
    
    . ${thisDir}/auxiliary/coregDirectoryErrorCheck
    
    # The high resolution is becoming the source,

    SOURCENAME=${HIRESNAME}
    SOURCEEXT=${HIRESEXT}
    
    debugout "HiRes name is : ${SOURCENAME}"   $SuperDebugFLAG
    debugout "- - - - - - - - - - - - - - - -" $SuperDebugFLAG
    # find and move it.
    . ${thisDir}/auxiliary/coregFindSourceAndMove

    # Now find the target, which is the overlay.

    TARGETNAME=${UMBatchMaster}/${SUBJDIR}/${subjects[$is]}/${fmriPATH}/${coregPATH}/${overlayNAME}
    TARGETEXT=${overlayExt}

    . ${thisDir}/auxiliary/verifyTargetImage

    debugout "Overlay name is : ${TARGETNAME}" $SuperDebugFLAG
    debugout "- - - - - - - - - - - - - - - -" $SuperDebugFLAG

  #
  # Make sure that now the HiRes and the OVERLAY image both exist.
  #
    echo "{ '${SOURCEIMG}','${TARGETIMG}' };..."         >> ${FULLSCRIPTNAME}.m
done

echo "                };"                                >> ${FULLSCRIPTNAME}.m

cd $curDIR

# Get the other images into the matlab script

. ${thisDir}/auxiliary/coregPrepOtherImages

# Wrap up the writing of the matlab script.

. ${thisDir}/auxiliary/coregPart_02

# Now build the shell script command that will get launched into the background.

# Common start to all shell scripts
. ${thisDir}/auxiliary/shellScriptStart

# Add the matlab code to the shell script

. ${thisDir}/auxiliary/shellScriptMATLABCall

# Finalize the shell script.

. ${thisDir}/auxiliary/shellScriptFinalize

# Now launch into the background if desired.

. ${thisDir}/auxiliary/shellScriptLaunch

#
# all done.
#