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antsN4SS
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antsN4SS
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#!/bin/bash
# # # # # # # # # # # # # # # # # #
#
# A command to make it easier on the user to skull strip
# and N4 the hires using ANTS
#
# This command will build a script to run and will also
# run the script in background.
#
# This was written with ANTS 2.3.1 as the testing
# context.
#
# e.g. antsN4SS
#
#
# Robert C. Welsh
# Copyright 2005-2019
#
# antsN4SS
#
#
#
#
# # # # # # # # # # # # # # # # # #
#
# Main antsN4SS function.
#
VERSION="1.0"
VERSIONDATE="2019-03-06"
# 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=" a B D d h M m odt t U w "
# This piece of code all of the spm12Batch scripts will use
. ${thisDir}/auxiliary/commonCode_AllScriptsStart
# This is the common in-line code for the warping steps.
. ${thisDir}/auxiliary/commonCode_ANTS_01
# This is common in-line code for all spm12Batch script to make sure arguments were passed
. ${thisDir}/auxiliary/commonCode_checkIfArgsPassed
# This is the common in-line code for the warping steps.
. ${thisDir}/auxiliary/commonCode_ANTS_02
#
# 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 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.
#
. ${thisDir}/auxiliary/antsHiRes_part_01
# Common star to all shell scripts
. ${thisDir}/auxiliary/buildMatlabScripts_01
. ${thisDir}/auxiliary/shellScriptStart
. ${thisDir}/auxiliary/antsCommonScript
# Now build the list of directories for each subject.
declare -i is
declare -i ii
curDIR=`pwd`
# Prepare the directory where the work is to take place.
echo " 4) prepping images"
for (( is=1 ; is<=$nSubjects ; is++ ))
do
cd ${UMBatchMaster}/${SUBJDIR}/${subjects[$is]}/
#
# create the newSeg directory.
#
debugout "- - - - - - - - - - - - - -" $SuperDebugFLAG
debugout "mkdir -p ${fmriPATH}/${coregPATH}/" $SuperDebugFLAG
debugout "- - - - - - - - - - - - - -" $SuperDebugFLAG
mkdir -p ${fmriPATH}/${coregPATH}/
debugout "- - - - - - - - - - - - - -" $SuperDebugFLAG
debugout "cd ${fmriPATH}/${coregPATH}/" $SuperDebugFLAG
debugout "- - - - - - - - - - - - - -" $SuperDebugFLAG
. ${thisDir}/auxiliary/coregDirectoryErrorCheck
# The hires is becoming the source,
SOURCENAME=${HIRESNAME}
SOURCEEXT=${HIRESEXT}
debugout "HiRes name is : ${SOURCENAME}" $SuperDebugFLAG
debugout "- - - - - - - - - - - - - - - -" $SuperDebugFLAG
# Copy the options file to the current working directory for invocation by the matlab code.
# We can reuse the vbm8 code here as there is nothing particular in vbm8FindSourceAndMove.
# this will take the specified high-resolution image set with the "-h" flag and stored in
# the variable FILENAME and processed by fileExtensionDetermination
# copies ${HIRES} to ${fmriPATH}/${coregPATH} from the ${anatomyPATH} directory
. ${thisDir}/auxiliary/vbm8FindSourceAndMove
done
echo " 5) building shell script"
echo
# Now put in some varibles needed
. ${thisDir}/auxiliary/antsHiRes_part_02
# Now build the shell script command that will get launched into the background.
. ${thisDir}/auxiliary/startBashSubjectLoop
# Add the ANTS code to the shell script
. ${thisDir}/auxiliary/antsN4SS_part_03
. ${thisDir}/auxiliary/endBashSubjectLoop
# Now add the call for creation of the mask -- needs to be modifed for ANTS
#. ${thisDir}/auxiliary/shellScriptErode
# Finalize the shell script.
. ${thisDir}/auxiliary/shellScriptFinalize
# Now launch into the background if desired.
. ${thisDir}/auxiliary/shellScriptLaunch
#
# all done.
#