Commit 8bc93897 authored by Amy Howard's avatar Amy Howard
Browse files

Delete run_NODDI_cleanup.sh

parent e5e9177e
#!/bin/sh
# Wrapper function to run NODDI
# AH Apr 2020
make_absolute(){
dir=$1;
if [ -d ${dir} ]; then
OLDWD=`pwd`
cd ${dir}
dir_all=`pwd`
cd $OLDWD
else
dir_all=${dir}
fi
echo ${dir_all}
}
Usage() {
echo ""
echo "Usage: run_NODDI.sh <subject_directory>"
echo ""
echo "expects to find estimated parameters in subject directory"
echo ""
echo "<options>:"
echo "-m (model = invivo/exvivo)"
exit 1
}
[ "$1" = "" ] && Usage
subjdir=`make_absolute $1`
model=invivo # default
shift
while [ ! -z "$1" ]
do
case "$1" in
-m) model=$2;shift;;
esac
shift
done
if [ -z "$model" ]; then
echo "Must specify model name as either 'invivo' or 'exvivo'"
exit 1
elif [ "$model" == "invivo" ]; then
export modelname=NODDI_Watson_diff
elif [ "$model" == "exvivo" ]; then
export modelname=NODDI_Watson_diff_exvivo
else
echo "Must specify model name as either 'invivo' or 'exvivo'"
exit 1
fi
outDir=${subjdir}.${modelname}
echo 'Converting cudimot output to NODDI variables'
/home/fs0/amyh/cudimot/mymodels/NODDI_Watson_diff/NODDI_Watson_finish.sh $outDir
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