Commit e6f754f0 authored by Amy Howard's avatar Amy Howard
Browse files

Delete run_NODDI.sh

parent a99c886c
#!/bin/sh
# Wrapper function to run NODDI
# AH Apr 2020
Usage() {
echo ""
echo "Usage: run_NODDI.sh <subject_directory> [options]"
echo ""
echo "expects to find data and nodif_brain_mask in subject directory"
echo ""
echo "<options>:"
echo "-m (model = invivo/exvivo)"
echo "--dax (axial diffusivity) "
echo "-Q (name of the GPU(s) queue, default cuda.q (defined in environment variable: FSLGECUDAQ)"
echo "-NJOBS (number of jobs to queue, the data is divided in NJOBS parts, usefull for a GPU cluster, default 4)"
echo "--runMCMC (if you want to run MCMC)"
echo "-b (burnin period, default 5000)"
echo "-j (number of jumps, default 1250)"
echo "-s (sample every, default 25)"
echo "--BIC_AIC (calculate BIC & AIC)"
echo ""
exit 1
}
[ "$1" = "" ] && Usage
modelname=NODDI_Watson
step1=GridSeach
step2=FitFractions
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${FSLDIR}/lib
subjdir=`make_absolute $1`
subjdir=`echo $subjdir | sed 's/\/$/$/g'`
echo "---------------------------------------------------------------------------------"
echo "------------------------------------ CUDIMOT ------------------------------------"
echo "----------------------------- MODEL: $modelname -----------------------------"
echo "---------------------------------------------------------------------------------"
echo subjectdir is $subjdir
start=`date +%s`
#parse option arguments
njobs=4
burnin=1000
njumps=1250
sampleevery=25
other=""
queue=""
lastStepModelOpts=""
shift
while [ ! -z "$1" ]
do
case "$1" in
-Q) queue="-q $2";shift;;
-NJOBS) njobs=$2;shift;;
-b) burnin=$2;shift;;
-j) njumps=$2;shift;;
-s) sampleevery=$2;shift;;
--runMCMC) lastStepModelOpts=$lastStepModelOpts" --runMCMC";;
--BIC_AIC) lastStepModelOpts=$lastStepModelOpts" --BIC_AIC";;
*) other=$other" "$1;;
esac
shift
done
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