Update run_NODDI.sh

run_NODDI.sh

-/Users/amyh/Desktop/func/run_NODDI.sh
\ No newline at end of file
+#!/bin/sh
+
+# Wrapper function to run NODDI
+# Can user specify both dax and diso on either in vivo or ex vivo model
+# 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> [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 "--diso (isotropic diffusivity) "
+    echo "--runMCMC (if you want to run MCMC)"
+    echo "--rician (if you want to run rician noise modelling during MCMC)"
+    echo "--getPredictedSignal	(save the predicted signal by the model at the end)"
+    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
+
+subjdir=`make_absolute $1`
+
+module add cuda/7.5
+. /opt/fmrib/fsl/etc/fslconf/fsl.sh
+export FSLCONFDIR=/opt/fmrib/fsl/config
+export FSLMACHTYPE=linux_64-gcc4.8
+export CUDA=/opt/cuda-7.5
+export FSLDEVDIR=/home/fs0/amyh/cudimot/fsl-dev
+export CUDIMOT=$FSLDEVDIR
+
+#parse option arguments
+njobs=4
+burnin=1000
+njumps=1250
+sampleevery=25
+other=""
+queue=""
+lastStepModelOpts=""
+model=invivo
+mcmc=0
+
+shift
+while [ ! -z "$1" ]
+do
+  case "$1" in
+      -m) model=$2;shift;;
+      --dax) dax=$2;shift;;
+      --diso) diso=$2;shift;;
+      -b) burnin=$2;shift;;
+      -j) njumps=$2;shift;;
+      -s) sampleevery=$2;shift;;
+      --runMCMC) mcmc=1;;
+      --rician) mcmc=1; lastStepModelOpts=$lastStepModelOpts" --rician";;
+      --BIC_AIC) lastStepModelOpts=$lastStepModelOpts" --BIC_AIC";;
+      --getPredictedSignal) lastStepModelOpts=$lastStepModelOpts" --getPredictedSignal";;
+      *) other=$other" "$1;;
+  esac
+  shift
+done
+
+if [ $mcmc -eq 1 ]; then
+    lastStepModelOpts=$lastStepModelOpts" --runMCMC"
+elif [ $mcmc -eq 0 ]; then
+    echo "Note: Rician noise modelling is not selected, though its use is recommended."
+fi
+
+if [ -z "$model" ]; then 
+    echo "Must specify model name as either 'invivo' or 'exvivo'"
+    exit 1
+elif [ "$model" == "invivo" ]; then
+    # Default params
+    if [ -z "$dax" ]; then dax=0.0017; fi
+    if [ -z "$diso" ]; then diso=0.003; fi
+    export modelname=NODDI_Watson_diff
+elif [ "$model" == "exvivo" ]; then
+    # Default params
+    if [ -z "$dax" ]; then dax=0.0006; fi       # No idea where these values come from
+    if [ -z "$diso" ]; then diso=0.002; fi
+    export modelname=NODDI_Watson_diff_exvivo
+else
+    echo "Must specify model name as either 'invivo' or 'exvivo'"
+    exit 1
+fi
+
+opts="--dax $dax --diso $diso -b $burnin -j $njumps -s $sampleevery"
+
+echo Please remember to cite Hernandez-Fernandez et al. Neuroimage 1019 if using this code.
+      
+/home/fs0/amyh/cudimot/mymodels/$modelname/Pipeline_${modelname}.sh $subjdir $opts $lastStepModelOpts