Delete run_NODDI.sh

NODDI_Watson_diff/development/run_NODDI.sh

-#!/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