despikeAFNI

#!/bin/bash

# # # # # # # # # # # # # # # # # # 
#
# A command to make it easier on the user to detect 
# spikes in the fmri time-series.
#
# This command will build a script to run and will also 
# run the script in background.
#
#   e.g.    despikeAFNI 
#
#
# despikeAFNI
#
# Expected is:
#
#        [task]/
#            run_01/
#                run_01.nii
#            run_02/
#                run_02.nii
#
# # # # # # # # # # # # # # # # # #

#
# Main detectSpike function.
#

VERSION="2.1"
VERSIONDATE="2021-03-23"

# 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 f 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 warping steps. ###
. ${thisDir}/auxiliary/commonCode_Despike_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

# 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 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/despikeAFNI_01

# Common start to all shell scripts

echo "    4) finalizing matlab scripts"

. ${thisDir}/auxiliary/buildMatlabScripts_01

. ${thisDir}/auxiliary/shellScriptStart

echo "    5) building shell script"

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

# Common start to all shell scripts

. ${thisDir}/auxiliary/despikeAFNI_part_02

. ${thisDir}/auxiliary/startBashSubjectLoop

# Add the distortion code to the shell script

cat ${thisDir}/auxiliary/despikeAFNI_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.
#