realignfMRI12

#!/bin/bash

# # # # # # # # # # # # # # # # # # 
#
#
# A batch routine to do slice-time correction
# using SPM12 Routines
#
#
# Robert C. Welsh
# Copyright 2006-2016
# Copyright 2017
#
#
# # # # # # # # # # # # # # # # # # 

#
# Main function of realignfMRI12
#

VERSION="1.0"
VERSIONDATE="2017-02-10"

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

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

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

# 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 D d f l M m on t U v "

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

# Validate that we have FSL installed.
. ${thisDir}/auxiliary/commonCode_RealignfMRI12

# 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

# Make the sandbox if possible.

. ${thisDir}/auxiliary/make_sandbox

#
# 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.

# 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/realignfMRI_01

# Now build the list of directories for each subject.

. ${thisDir}/auxiliary/createDirectoryList

echo "    4) finalizing matlab scripts"

cat ${thisDir}/parts/realignfMRI_part_2.m                         >> ${FULLSCRIPTNAME}.m

echo "    5) building shell script"

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

# Now create verify that the sandbox is there.

. ${thisDir}/auxiliary/shellScriptCreateSandBox

# 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.
#