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Cleaned up the options parsing a little. #2

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Cleaned up the options parsing a little. #2

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78 changes: 20 additions & 58 deletions NODDI/gbss_1_reg.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -52,68 +52,30 @@ exit 1
}


if [ -z "${FSLDIR}" ]; then
echo "FSLDIR is not set. Please load your FSL environment before continuing."
exit 1;
fi

#Setting Defaults
method=1;
template="${FSLDIR}/MNI152_T1_1mm.nii.gz"
atropos_method=1;
ants_number=4;
mrf=0.3;
prior=0.2;

while getopts ":c:t:w:n:f:p:h" OPT; do
case $OPT in

c) #template method

method=$OPTARG

if [[ ${#method} == 0 ]] ; then

echo "Using a pre-existing template file..."

fi

;;

t) # getopts issues an error message

template=$OPTARG

;;

w) # getopts issues an error message

atropos_method=$OPTARG

;;
n) # getopts issues an error message

ants_number=$OPTARG
;;
f) # getopts issues an error message

mrf=$OPTARG

;;
p) # getopts issues an error message

prior=$OPTARG

;;
h) #help

usage
exit 1;
;;
*) # getopts issues an error message

usage

exit 1

;;

c) method=$OPTARG ;;
t) template=$OPTARG ;;
w) atropos_method=$OPTARG ;;
n) ants_number=$OPTARG ;;
f) mrf=$OPTARG ;;
p) prior=$OPTARG ;;
h) usage; exit 1 ;;
*) usage; exit 1 ;;
esac

done

shift $((OPTIND-1))
Expand All @@ -122,19 +84,19 @@ out_dir=$1 #output directory
[ "$out_dir" = "" ] && usage

echo "List of parameters:"
echo "prior=$prior"
echo "ANTS Method=$atropos_method"
echo "Template File: $template"
echo "MRF=$mrf"
echo "Template method: $method"
echo "ANTS Method: $atropos_method"
echo "Prior: $prior"
echo "Template File: $template"
echo "MRF: $mrf"
echo "Output directory: $out_dir"

###############################################################
################# PART 1.1: Making Directories ################
###############################################################

#making output directory/subdirectories for the analysis

mkdir ${out_dir}/tmpsapce
mkdir ${out_dir}/tmpspace -p # -p makes the folder, and parents

###############################################################
################## PART 1.2: tbss_1_preproc ###################
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