Delete Pipeline_NODDI_Watson.sh

NODDI_Watson_diff/development/Pipeline_NODDI_Watson.sh

-#!/bin/sh
-#
-#   Moises Hernandez-Fernandez - FMRIB Image Analysis Group
-#
-#   Copyright (C) 2004 University of Oxford
-#
-#   SHCOPYRIGHT
-#
-# Pipeline for fitting NODDI-Watson 
-
-if [ "x$CUDIMOT" == "x" ]; then
-	echo ""
-	echo "Please, set enviroment variable CUDIMOT with the path where cuDIMOT is installed"
-	echo "The path must contain a bin directory with binary files, i.e. \$CUDIMOT/bin"
-	echo "For instance:   export CUDIMOT=/home/moises/CUDIMOT"
-	echo ""
-  exit 1
-fi
-
-bindir=${CUDIMOT}/bin
-
-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: Pipeline_NODDI_Watson.sh <subject_directory> [options]"
-    echo ""
-    echo "expects to find data and nodif_brain_mask in subject directory"
-    echo ""
-    echo "<options>:"
-    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" "$1;;
-  esac
-  shift
-done
-
-#Set options
-opts="--bi=$burnin --nj=$njumps --se=$sampleevery"
-opts="$opts $other"
-
-if [ "x$SGE_ROOT" != "x" ]; then
-	queue="-q $FSLGECUDAQ"
-fi
-
-#check that all required files exist
-
-if [ ! -d $subjdir ]; then
-	echo "subject directory $1 not found"
-	exit 1
-fi
-
-if [ `${FSLDIR}/bin/imtest ${subjdir}/data` -eq 0 ]; then
-	echo "${subjdir}/data not found"
-	exit 1
-fi
-
-if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif_brain_mask` -eq 0 ]; then
-	echo "${subjdir}/nodif_brain_mask not found"
-	exit 1
-fi
-
-if [ -e ${subjdir}.${modelname}/xfms/eye.mat ]; then
-	echo "${subjdir} has already been processed: ${subjdir}.${modelname}." 
-	echo "Delete or rename ${subjdir}.${modelname} before repeating the process."
-	exit 1
-fi
-
-echo Making output directory structure
-
-mkdir -p ${subjdir}.${modelname}/
-mkdir -p ${subjdir}.${modelname}/diff_parts
-mkdir -p ${subjdir}.${modelname}/logs
-mkdir -p ${subjdir}.${modelname}/Dtifit
-mkdir -p ${subjdir}.${modelname}/${step1}
-mkdir -p ${subjdir}.${modelname}/${step1}/diff_parts
-mkdir -p ${subjdir}.${modelname}/${step1}/logs
-mkdir -p ${subjdir}.${modelname}/${step2}
-mkdir -p ${subjdir}.${modelname}/${step2}/diff_parts
-mkdir -p ${subjdir}.${modelname}/${step2}/logs
-part=0
-
-echo Copying files to output directory
-
-${FSLDIR}/bin/imcp ${subjdir}/nodif_brain_mask ${subjdir}.${modelname}
-if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif` = 1 ] ; then
-    ${FSLDIR}/bin/fslmaths ${subjdir}/nodif -mas ${subjdir}/nodif_brain_mask ${subjdir}.${modelname}/nodif_brain
-fi
-
-# Specify Common Fixed Parameters
-CFP_file=$subjdir.${modelname}/CFP
-cp ${subjdir}/bvecs $subjdir.${modelname}
-cp ${subjdir}/bvals $subjdir.${modelname}
-echo  $subjdir.${modelname}/bvecs > $CFP_file
-echo  $subjdir.${modelname}/bvals >> $CFP_file
-
-#Set more options
-opts=$opts" --data=${subjdir}/data --maskfile=$subjdir.${modelname}/nodif_brain_mask --forcedir --CFP=$CFP_file"
-
-# Calculate S0 with the mean of the volumes with bval<50
-bvals=`cat ${subjdir}/bvals`
-mkdir -p ${subjdir}.${modelname}/temporal
-pos=0
-for i in $bvals; do 
-    if [ $i -le 50 ]; then  
-       	fslroi ${subjdir}/data  ${subjdir}.${modelname}/temporal/volume_$pos $pos 1    
-    fi 
-    pos=$(($pos + 1))
-done
-fslmerge -t ${subjdir}.${modelname}/temporal/S0s ${subjdir}.${modelname}/temporal/volume*
-fslmaths ${subjdir}.${modelname}/temporal/S0s -Tmean ${subjdir}.${modelname}/S0
-rm -rf ${subjdir}.${modelname}/temporal
-
-# Specify Fixed parameters: S0
-FixPFile=${subjdir}.${modelname}/FixP
-echo ${subjdir}.${modelname}/S0 >> $FixPFile
-
-##############################################################################
-################################ First Dtifit  ###############################
-##############################################################################
-echo "Queue Dtifit"
-PathDTI=${subjdir}.${modelname}/Dtifit
-dtifit_command="${bindir}/Run_dtifit.sh ${subjdir} ${subjdir}.${modelname} ${bindir}"
-#SGE
-dtifitProcess=`${FSLDIR}/bin/fsl_sub $queue -l $PathDTI/logs -N dtifit $dtifit_command`
-
-##### Model Parameters: fiso, fintra, kappa, th, ph  ######
-#############################################################
-##################### Grid Search Step ######################
-#############################################################
-echo "Queue GridSearch process"
-PathStep1=$subjdir.${modelname}/${step1}
-
-# Create file to specify initialisation parameters (2 parameters: th,ph)
-InitializationFile=$PathStep1/InitializationParameters
-echo "" > $InitializationFile #fiso
-echo "" >> $InitializationFile #fintra
-echo "" >> $InitializationFile #kappa
-echo ${PathDTI}/dtifit_V1_th.nii.gz >> $InitializationFile #th
-echo ${PathDTI}/dtifit_V1_ph.nii.gz >> $InitializationFile #ph
-
-# Do GridSearch (fiso,fintra,kappa)
-GridFile=$PathStep1/GridSearch
-echo "search[0]=(0.0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0)" > $GridFile #fiso
-echo "search[1]=(0.0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0)" >> $GridFile #fintra
-echo "search[2]=(1,2,3,4,5,6,7,8)" >> $GridFile #kappa
-
-partsdir=$PathStep1/diff_parts
-outputdir=$PathStep1
-Step1Opts=$opts" --outputdir=$outputdir --partsdir=$partsdir --FixP=$FixPFile --gridSearch=$GridFile --no_LevMar --init_params=$InitializationFile --fixed=3,4"
-
-postproc=`${bindir}/jobs_wrapper.sh $PathStep1 $dtifitProcess $modelname GS $njobs $Step1Opts`
-
-###############################################################
-##################### Fit only Fractions ######################
-###############################################################
-echo "Queue Fitting Fractions process"
-PathStep2=$subjdir.${modelname}/${step2}
-
-# Create file to specify initialisation parameters (2 parameters: fiso,fintra)
-InitializationFile=$PathStep2/InitializationParameters
-echo $PathStep1/Param_0_samples > $InitializationFile #fiso
-echo $PathStep1/Param_1_samples >> $InitializationFile #fintra
-echo $PathStep1/Param_2_samples >> $InitializationFile #kappa
-echo ${PathDTI}/dtifit_V1_th.nii.gz >> $InitializationFile #th
-echo ${PathDTI}/dtifit_V1_ph.nii.gz >> $InitializationFile #ph
-
-partsdir=$PathStep2/diff_parts
-outputdir=$PathStep2
-Step2Opts=$opts" --outputdir=$outputdir --partsdir=$partsdir --FixP=$FixPFile --init_params=$InitializationFile --fixed=2,3,4"
-
-postproc=`${bindir}/jobs_wrapper.sh $PathStep2 $postproc $modelname FitFractions $njobs $Step2Opts`
-
-######################################################################################
-######################### Fit all the parameters of the Model ########################
-######################################################################################
-echo "Queue Fitting process"
-
-# Create file to specify initialization parameters (5 parameters: fiso,fintra,kappa,th,ph)
-InitializationFile=$subjdir.${modelname}/InitializationParameters
-echo $PathStep2/Param_0_samples > $InitializationFile #fiso
-echo $PathStep2/Param_1_samples >> $InitializationFile #fintra
-echo ${PathStep1}/Param_2_samples >> $InitializationFile #kappa
-echo ${PathDTI}/dtifit_V1_th.nii.gz >> $InitializationFile #th
-echo ${PathDTI}/dtifit_V1_ph.nii.gz  >> $InitializationFile #ph
-
-partsdir=${subjdir}.${modelname}/diff_parts
-outputdir=${subjdir}.${modelname}
-ModelOpts=$opts" --outputdir=$outputdir --partsdir=$partsdir --FixP=$FixPFile --init_params=$InitializationFile $lastStepModelOpts"
-
-postproc=`${bindir}/jobs_wrapper.sh ${subjdir}.${modelname} $postproc $modelname FitProcess $njobs $ModelOpts`
-
-#########################################
-### Calculate Dispersion Index & dyads ###
-##########################################
-finish_command="${bindir}/${modelname}_finish.sh ${subjdir}.${modelname}"
-#SGE
-finishProcess=`${FSLDIR}/bin/fsl_sub $queue -l ${subjdir}.${modelname}/logs -N ${modelname}_finish -j $postproc $finish_command`
-
-endt=`date +%s`
-runtime=$((endt-start))
-#echo Runtime $runtime
-echo Everything Queued