spm12Batch_CheckInstall

#!/bin/bash

# # # # # # # # # # # # # # # # # # 
#
# Run this command to check if the install is okay
#
# This is a brief check, best is to run the
# preprocessing example for TestSubject.
#
#   e.g.   spm12Batch_CheckInstall
#
#
#                         Robert C. Welsh
#                         Copyright 2005-2021
#
# spm12Batch_CheckInstall
#
# # # # # # # # # # # # # # # # # #

#
# Main spm23Batch function.
#

VERSION="1.0"
VERSIONDATE="2021-04-12"

# 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}'`

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

# We only will print out the help and ignore everything!

#. ${thisDir}/auxiliary/help/${thisCommand}_Help

# Check for directories.

PROB=0

SPM12BATCHOK="spm12Batch and necessary elements appear all okay."
for ITEM in ${SPM12B1} ${SPM12B3}
do
    if [ ! -d ${ITEM} ]
    then       
	echo "Element missing : ${ITEM}"
	SPM12BATCHOK="spm12Batch and necessary elements appear to have a problem."
	PROB=1
    fi
done

# Check for executables.

for ITEM in ${MATLAB} 3dDespike fslorient animaDistortionCorrection antsRegistration 
do
    THERE=`which ${ITEM}`
    if [ -z "${THERE}" ]
    then
	echo "Element missing : ${ITEM}"
	SPM12BATCHOK="spm12Batch and necessary elements appear to have a problem."
	PROB=$(( ${PROB} + 1 ))
    fi
done
	    
# Check the the MICCAI is there

ANTSdir=`which antsRegistration`
if [ ! -z "${ANTSdir}" ]
then
    ANTSdir=`dirname ${ANTSdir}`
    if [ ! -d ${ANTSdir}/../Templates/MICCAI2012-Multi-Atlas-Challenge-Data ]
    then
	echo
	echo "Missing MICCAI templates for ANTs, see Installation instructions for the Administrator."
	if [ ${PROB} -eq 0 ]
	   then
	       SPM12BATCHOK="spm12Batch and binaries are okay, but see the issue above."
	fi
    fi
else
    echo
    echo "Missing ANTs"  
fi


echo
echo ${SPM12BATCHOK}
echo

exit 0

#
# all done.
#