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main.sh
executable file
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main.sh
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#!/bin/bash
# Written by Andreas Heckel
# University of Heidelberg
# https://github.com/ahheckel
# 12/01/2012
export LC_ALL=C # set locale to C (ensures proper sorting)
echo "---------------------------"
# is another instance running ?
if [ -d $(dirname $0)/.lockdir121978 ] ; then echo "$0 : --> another instance is already running - exiting." ; exit 1 ; fi
# start in background mode ?
if [ x"$1" = "xbg" ] ; then
trap 'echo -e "\n********************\nTo cancel background job type \n kill $(cat ./log | grep Job | cut -d : -f 2)\n\nTo view logfile type \n tail -f log\n"********************' EXIT
cd $(dirname $0)
nohup ./run_script.sh &> log &
tail -f log
exit 0
fi
# check if superuser
if [ "$(id -u)" = "0" ]; then
echo "$(basename $0): This script must not be run as root !" 1>&2
exit 1
fi
# echo date
startdate=$(date) ; echo "'$0' started on ${startdate}."
startdate_sec=$(date +"%s")
# exit on error
set -e
# define error trap
trap 'finishdate_sec=$(date +"%s") ; diff=$(($finishdate_sec-$startdate_sec)) ; echo "$0 : An ERROR has occured on `date` (Job-Id : $$). Time elapsed since start: $(echo "scale=4 ; $diff / 3600" | bc -l) h ($(echo "scale=0 ; $diff / 60" | bc -l) min)"' ERR # don't exit on trap (!)
# define and change to working directory
wd=$(dirname $0); cd $wd ; wd=`pwd`
# display FSL version
if [ x$FSL_DIR = "x" ] ; then FSL_DIR="$FSLDIR" ; fi
if [ x$FSL_DIR = "x" ] ; then echo "ERROR : \$FSL_DIR and \$FSLDIR variable not defined - exiting." ; exit 1 ; fi
fslversion=$(cat $(dirname $(dirname `which imglob`))/etc/fslversion)
echo ""; echo "FSL version is '${fslversion}'." ; # sleep 1
# display FREESURFER version
echo "FREESURFER build-stamp is '`cat $FREESURFER_HOME/build-stamp.txt`'." ; echo ""
# display Job-Id
echo "Job-Id : $$" ; echo ""
# source environment variables
if [ ! -f ./globalvars ] ; then echo "ERROR: 'globalvars' not found - exiting." ; exit 1 ; fi
source ./globalvars
# define subdirs
scriptdir=$studydir/rsc/scripts
tmpltdir=$studydir/rsc/scripts/templates
tmpdir=$studydir/.tmp
# make temp directory
mkdir -p $tmpdir
# source environment functions
source $scriptdir/globalfuncs
# check for RAM dumps
dumps=$(find ./ -maxdepth 2 -name "core*")
#dumps=$(find ./ -name "core*")
if [ $(echo $dumps | wc -w) -gt 0 ] ; then
echo "ERROR: memory dumps (core-files) detected - you should look into this. Exiting... "
echo $dumps | row2col
exit 1
fi
# export JOB-ID variable and check if fsl_sub is patched accordingly
if [ $(cat `which fsl_sub` | grep GRID_JOB_ID_FILE | grep HKL | wc -l) -eq 3 -a x"$SGE_ROOT" != "x" ] ; then
echo -n "NOTE: fsl_sub is patched for job control ; "
GRID_JOB_ID_FILE=$wd/.jid.grid.$$
echo "touching job-ID file '$GRID_JOB_ID_FILE'"
touch $GRID_JOB_ID_FILE
export GRID_JOB_ID_FILE
elif [ $(cat `which fsl_sub` | grep GRID_JOB_ID_FILE | grep HKL | wc -l) -lt 3 -a x"$SGE_ROOT" != "x" ] ; then
echo "ERROR: fsl_sub is NOT patched for job control! Exiting... " ; exit 1
fi
# check if FREESURFER's fsl_sub is patched
for fs_fsl_sub in $FREESURFER_HOME/bin/fsl_sub_mgh FREESURFER_HOME/bin/fsl_sub_seychelles ; do
if [ -f $fs_fsl_sub ] ; then
if [ "$(readlink $fs_fsl_sub)" = "$FSLDIR/bin/fsl_sub" ] ; then
echo "NOTE: '$fs_fsl_sub' is linked to '$FSLDIR/bin/fsl_sub'"
else
echo "ERROR: '$fs_fsl_sub' is NOT linked to '$FSLDIR/bin/fsl_sub'! Exiting... " ; exit 1
fi
fi
done
echo ""
# create and check lock
set +e
lock="$wd/.lockdir121978"
echo "creating lock [ '$lock' ]"
mkdir $lock &>/dev/null
if [ $? -gt 0 ] ; then echo "$0 : --> another instance is already running - exiting." ; exit 1 ; fi
lock=""
echo ""
set -e
# create subjects-dir.
mkdir -p $subjdir
# remove lock on exit
trap 'set +e ; echo --------------------------- ; delJIDs $GRID_JOB_ID_FILE ; save_config $studydir $subjdir "$startdate" ; rmdir $wd/.lockdir121978 ; echo "Lock removed." ; time_elapsed $startdate_sec ; echo "Exiting on `date`" ; echo --------------------------- ; exit' EXIT
# remove duplicates in string arrays (to avoid collisions on the cluster)
FIRSTLEV_SUBJECTS=$(echo $FIRSTLEV_SUBJECTS | row2col | sort -u)
FIRSTLEV_SESSIONS_FUNC=$(echo $FIRSTLEV_SESSIONS_FUNC | row2col | sort -u)
FIRSTLEV_SESSIONS_STRUC=$(echo $FIRSTLEV_SESSIONS_STRUC | row2col | sort -u)
SECONDLEV_SUBJECTS=$(echo $SECONDLEV_SUBJECTS_SUBJECTS | row2col | sort -u)
SECONDLEV_SESSIONS_FUNC=$(echo $SECONDLEV_SUBJECTS_SESSIONS_FUNC | row2col | sort -u)
SECONDLEV_SESSIONS_STRUC=$(echo $SECONDLEV_SUBJECTS_SESSIONS_STRUC | row2col | sort -u)
BOLD_SLICETIMING_VALUES=$(echo $BOLD_SLICETIMING_VALUES | row2col | sort -u)
BOLD_SMOOTHING_KRNLS=$(echo $BOLD_SMOOTHING_KRNLS | row2col | sort -u)
BOLD_HPF_CUTOFFS=$(echo $BOLD_HPF_CUTOFFS | row2col | sort -u)
BOLD_DENOISE_SMOOTHING_KRNLS=$(echo $BOLD_DENOISE_SMOOTHING_KRNLS | row2col | sort -u)
BOLD_DENOISE_MASKS_NAT=$(echo $BOLD_DENOISE_MASKS_NAT | row2col | sort -u)
BOLD_DENOISE_MASKS_MNI=$(echo $BOLD_DENOISE_MASKS_MNI | row2col | sort -u)
BOLD_DENOISE_USE_MOVPARS_NAT=$(echo $BOLD_DENOISE_USE_MOVPARS_NAT | row2col | sort -u)
BOLD_DENOISE_USE_MOVPARS_MNI=$(echo $BOLD_DENOISE_USE_MOVPARS_MNI | row2col | sort -u)
BOLD_MNI_RESAMPLE_FUNCDATAS=$(echo $BOLD_MNI_RESAMPLE_FUNCDATAS | row2col | sort -u)
BOLD_MNI_RESAMPLE_RESOLUTIONS=$(echo $BOLD_MNI_RESAMPLE_RESOLUTIONS | row2col | sort -u)
ALFF_DENOISE_MASKS_NAT=$(echo $ALFF_DENOISE_MASKS_NAT | row2col | sort -u)
ALFF_DENOISE_USE_MOVPARS_NAT=$(echo $ALFF_DENOISE_USE_MOVPARS_NAT | row2col | sort -u)
ALFF_RESAMPLING_RESOLUTIONS=$(echo $ALFF_RESAMPLING_RESOLUTIONS | row2col | sort -u)
ALFF_INCLUDED_SUBJECTS=$(echo $ALFF_INCLUDED_SUBJECTS | row2col | sort -u)
ALFF_INCLUDED_SESSIONS=$(echo $ALFF_INCLUDED_SESSIONS | row2col | sort -u)
TBSS_INCLUDED_SUBJECTS=$(echo $TBSS_INCLUDED_SUBJECTS | row2col | sort -u)
TBSS_INCLUDED_SESSIONS=$(echo $TBSS_INCLUDED_SESSIONS | row2col | sort -u)
TBSS_THRES=$(echo $TBSS_THRES | row2col | sort -u)
FS_STATS_MEASURES=$(echo $FS_STATS_MEASURES | row2col | sort -u)
FS_STATS_SMOOTHING_KRNLS=$(echo $FS_STATS_SMOOTHING_KRNLS | row2col | sort -u)
VBM_INCLUDED_SUBJECTS=$(echo $VBM_INCLUDED_SUBJECTS | row2col | sort -u)
VBM_INCLUDED_SESSIONS=$(echo $VBM_INCLUDED_SESSIONS | row2col | sort -u)
VBM_SMOOTHING_KRNL=$(echo $VBM_SMOOTHING_KRNL | row2col | sort -u)
MELODIC_INCLUDED_SUBJECTS=$(echo $MELODIC_INCLUDED_SUBJECTS | row2col | sort -u)
MELODIC_INCLUDED_SESSIONS=$(echo $MELODIC_INCLUDED_SESSIONS | row2col | sort -u)
MELODIC_CMD_INPUT_FILES=$(echo $MELODIC_CMD_INPUT_FILES | row2col | sort -u)
MELODIC_CMD_INCLUDED_SUBJECTS=$(echo $MELODIC_CMD_INCLUDED_SUBJECTS | row2col | sort -u)
MELODIC_CMD_INCLUDED_SESSIONS=$(echo $MELODIC_CMD_INCLUDED_SESSIONS | row2col | sort -u)
DUALREG_INCLUDED_SUBJECTS=$(echo $DUALREG_INCLUDED_SUBJECTS | row2col | sort -u)
DUALREG_INCLUDED_SESSIONS=$(echo $DUALREG_INCLUDED_SESSIONS | row2col | sort -u)
DUALREG_INPUT_ICA_DIRNAMES=$(echo $DUALREG_INPUT_ICA_DIRNAMES | row2col | sort -u)
DUALREG_IC_FILENAMES=$(echo $DUALREG_IC_FILENAMES | row2col | sort -u)
DUALREG_INPUT_BOLD_FILES=$(echo $DUALREG_INPUT_BOLD_FILES | row2col | sort -u)
DUALREG_USE_MOVPARS_HPFS=$(echo $DUALREG_USE_MOVPARS_HPFS | row2col | sort -u)
DUALREG_USE_MOVPARS_TYPES=$(echo $DUALREG_USE_MOVPARS_TYPES | row2col | sort -u)
FSLNETS_DREGDIRS=$(echo $FSLNETS_DREGDIRS | row2col | sort -u)
# define denoise tags
_m=$(for i in $BOLD_DENOISE_MASKS_NAT ; do remove_ext $i | cut -d _ -f 2 ; done) ; dntag_boldnat=$(rem_blanks "$BOLD_DENOISE_USE_MOVPARS_NAT")$(rem_blanks "$_m")
_m=$(for i in $BOLD_DENOISE_MASKS_MNI ; do remove_ext $i | cut -d _ -f 2 ; done) ; dntag_boldmni=$(rem_blanks "$BOLD_DENOISE_USE_MOVPARS_MNI")$(rem_blanks "$_m")
_m=$(for i in $ALFF_DENOISE_MASKS_NAT ; do remove_ext $i | cut -d _ -f 2 ; done) ; dntag_alff=$(rem_blanks "$ALFF_DENOISE_USE_MOVPARS_NAT")$(rem_blanks "$_m")
# ----- create 1st level subject- and session files -----
if [ "x$FIRSTLEV_SUBJECTS" != "x" -a "x$FIRSTLEV_SESSIONS_FUNC" != "x" -a "x$FIRSTLEV_SESSIONS_STRUC" != "x" ] ; then
echo "creating subjects file..."
#errflag=0
#for i in $FIRSTLEV_SUBJECTS ; do if [ ! -d ${subjdir}/$i ] ; then errflag=1 ; echo "ERROR: '${subjdir}/$i' does not exist!" ; fi ; done
#if [ $errflag -eq 1 ] ; then echo "...exiting." ; exit 1 ; fi
echo $FIRSTLEV_SUBJECTS | row2col > ${subjdir}/subjects
cat -n ${subjdir}/subjects
echo ""
for subj in `cat ${subjdir}/subjects` ; do
if [ ! -d ${subjdir}/$subj ] ; then mkdir -p ${subjdir}/$subj ; fi
echo "creating functional session file for subject '$subj': "[ $FIRSTLEV_SESSIONS_FUNC ]""
echo $FIRSTLEV_SESSIONS_FUNC | row2col > ${subjdir}/$subj/sessions_func
echo "creating structural session file for subject '$subj': "[ $FIRSTLEV_SESSIONS_STRUC ]""
echo $FIRSTLEV_SESSIONS_STRUC | row2col > ${subjdir}/$subj/sessions_struc
done
echo ""
fi
# ----- CHECKS -----
# are all required progs / files installed ?
$scriptdir/_check_progs.sh ; echo ""
## make scripts executable
#dos2unix -q $scriptdir/*
#chmod +x $scriptdir/*.sh
# check presence of info files
if [ $CHECK_INFOFILES = 1 ] ; then
# is subjects file present ?
if [ ! -f ${subjdir}/subjects ] ; then
echo "Subjects file not present - proposal:"
cd $subjdir
files=`find ./?* -maxdepth 0 -type d | sort | cut -d / -f 2 | grep -v $(basename $FS_subjdir) | grep -v $(basename $FS_sessdir)`
for i in $files ; do echo $i ; done
read -p "Press Key to accept these entries, otherwise abort with Conrol-C..."
echo $files | row2col > subjects
files=""
cd $wd
fi
# is sessions file present ? (in case of multisession designs)
for subj in `cat ${subjdir}/subjects` ; do
if [ ! -f $subjdir/$subj/sessions_struc -o ! -f $subjdir/$subj/sessions_func ] ; then
if [ $(find $subjdir/$subj/ -maxdepth 1 -type d | wc -l) -eq 1 ] ; then
echo "WARNING : No session files detected. Since no subdirectories in $subjdir/$subj were detected -> assuming single session design. Now creating empty session files..."
echo '.' > $subjdir/$subj/sessions_struc
echo '.' > $subjdir/$subj/sessions_func
echo "done."
fi
fi
if [ ! -f ${subjdir}/${subj}/sessions_struc ] ; then
read -p "Session File for structural processing not present in ${subjdir}/${subj}. You will need to create that file. Exiting..." ; exit 1 ;
fi
if [ ! -f ${subjdir}/${subj}/sessions_func ] ; then
read -p "Session File for functional processing not present in ${subjdir}/${subj}. You will need to create that file. Exiting..." ; exit 1 ;
fi
done
# are bet info present ?
if [ ! -f ${subjdir}/config_bet_lowb ] ; then
read -p "Bet info file for the diffusion images not present in ${subjdir}. Press Key to create the default template."
for subj in `cat $subjdir/subjects`; do for sess in `cat $subjdir/$subj/sessions_struc` ; do echo "$(subjsess) $BETLOWB_INFO" | tee -a $subjdir/config_bet_lowb ; done ; done
fi
if [ ! -f ${subjdir}/config_bet_magn ] ; then
read -p "Bet info file for the magnitude images not present in ${subjdir}. Press Key to create the default template."
for subj in `cat $subjdir/subjects`; do for sess in `cat $subjdir/$subj/sessions_* | sort | uniq` ; do echo "$(subjsess) $BETMAGN_INFO" | tee -a $subjdir/config_bet_magn ; done ; done
fi
if [ ! -f ${subjdir}/config_bet_struc0 ] ; then
read -p "Bet info file for the structural images (prae - std. space masking) not present in ${subjdir}. Press Key to create the default template."
for subj in `cat $subjdir/subjects`; do for sess in `cat $subjdir/$subj/sessions_struc` ; do echo "$(subjsess) $BETSTRUC0_INFO" | tee -a $subjdir/config_bet_struc0 ; done ; done
fi
if [ ! -f ${subjdir}/config_bet_struc1 ] ; then
read -p "Bet info file for the structural images (post - std. space masking) not present in ${subjdir}. Press Key to create the default template."
for subj in `cat $subjdir/subjects`; do for sess in `cat $subjdir/$subj/sessions_struc` ; do echo "$(subjsess) $BETSTRUC1_INFO" | tee -a $subjdir/config_bet_struc1 ; done ; done
fi
if [ ! -f ${subjdir}/config_unwarp_dwi ] ; then
read -p "DWI-unwarp info file for diffusion images not present in ${subjdir}. Press Key to create the default template."
for subj in `cat $subjdir/subjects`; do for sess in `cat $subjdir/$subj/sessions_struc` ; do echo "$(subjsess) $DWIUNWARP_INFO" | tee -a $subjdir/config_unwarp_dwi ; done ; done
fi
if [ ! -f ${subjdir}/config_unwarp_bold ] ; then
read -p "BOLD-unwarp info file not present in ${subjdir}. Press Key to create the default template."
for subj in `cat $subjdir/subjects`; do for sess in `cat $subjdir/$subj/sessions_func` ; do echo "$(subjsess) $BOLDUNWARP_INFO" | tee -a $subjdir/config_unwarp_bold ; done ; done
fi
# check acquisition-parameter files
if [ ! -f ${subjdir}/config_acqparams_bold ] ; then
read -p "BOLD acquisition parameter info file not present in ${subjdir}. Press Key to create a template."
err=0 ;
if [ x$TR_bold = x ] ; then echo "ERROR: TR not defined (need dummy at least)." ; err=1 ; fi
if [ x$TE_bold = x ] ; then echo "ERROR: TE not defined (need dummy at least)." ; err=1 ; fi
if [ x$EES_bold = x ] ; then echo "ERROR: ESP not defined (need dummy at least)." ; err=1 ; fi
if [ $err -eq 1 ] ; then exit 1 ; fi
printf "#ID\t TR (s)\t TE (ms)\t EES (ms)\n" > ${subjdir}/config_acqparams_bold
for subj in `cat $subjdir/subjects`; do for sess in `cat $subjdir/$subj/sessions_func` ; do printf "$(subjsess)\t $TR_bold\t $TE_bold\t $EES_bold\n" | tee -a $subjdir/config_acqparams_bold ; done ; done
fi
if [ ! -f ${subjdir}/config_acqparams_dwi ] ; then
read -p "DWI acquisition parameter info file not present in ${subjdir}. Press Key to create a template."
err=0 ;
if [ x$TR_diff = x ] ; then echo "ERROR: TR not defined (need dummy at least)." ; err=1 ; fi
if [ x$TE_diff = x ] ; then echo "ERROR: TE not defined (need dummy at least)." ; err=1 ; fi
if [ x$EES_diff = x ] ; then echo "ERROR: ESP not defined (need dummy at least)." ; err=1 ; fi
if [ x$TROT_topup = x ] ; then echo "ERROR: TROT (topup) not defined (need dummy at least)." ; err=1 ; fi
if [ $err -eq 1 ] ; then exit 1 ; fi
printf "#ID\t TR (s)\t TE (ms)\t EES (ms)\t TOPUP-TROT (s)\n" > ${subjdir}/config_acqparams_dwi
for subj in `cat $subjdir/subjects`; do for sess in `cat $subjdir/$subj/sessions_struc` ; do printf "$(subjsess)\t $TR_diff\t $TE_diff\t $EES_diff\t $TROT_topup\n" | tee -a $subjdir/config_acqparams_dwi ; done ; done
fi
# are params defined as global variables ? if vars are empty -> set flag, so that params are retrieved from info files.
getTR_bold=0 ; getTE_bold=0 ; getEES_bold=0
getTR_diff=0 ; getTE_diff=0 ; getEES_diff=0 ; getTROT_topup=0
if [ x$TR_bold = x ] ; then getTR_bold=1 ; fi
if [ x$TE_bold = x ] ; then getTE_bold=1 ; fi
if [ x$EES_bold = x ] ; then getEES_bold=1 ; fi
if [ x$TR_diff = x ] ; then getTR_diff=1 ; fi
if [ x$TE_diff = x ] ; then getTE_diff=1 ; fi
if [ x$EES_diff = x ] ; then getEES_diff=1 ; fi
if [ x$TROT_topup = x ] ; then getTROT_topup=1 ; fi
echo "checking acquisition parameters in info files..."
for subj in `cat $subjdir/subjects`; do
for sess in `cat $subjdir/$subj/sessions_func` ; do
#echo "subj $subj , sess $sess : checking '$subjdir/config_acqparams_bold'"
defineBOLDparams $subjdir/config_acqparams_bold $subj $sess
done
done
for subj in `cat $subjdir/subjects`; do
for sess in `cat $subjdir/$subj/sessions_struc` ; do
#echo "subj $subj , sess $sess : checking '$subjdir/config_acqparams_dwi'"
defineDWIparams $subjdir/config_acqparams_dwi $subj $sess
done
done
echo "...done." ; echo ""
# is registration mapping file present ?
if [ ! -f ${subjdir}/config_func2highres.reg ] ; then
echo "WARNING: Registration mapping between functionals and t1 structural not found -> file created. You may need to edit that file..."
touch ${subjdir}/config_func2highres.reg
fi
# are template files present?
if [ ! -f ${tmpltdir}/template_tracula.rc ] ; then
read -p "TRACULA template file not found. You may need to create that file..."
fi
if [ ! -f ${tmpltdir}/template_preprocBOLD.fsf ] ; then
read -p "FEAT template file for BOLD preprocessing not found. You may need to create that file..."
fi
if [ ! -f ${tmpltdir}/template_makeXfmMatrix.m ] ; then
read -p "WARNING: OCTAVE file 'template_makeXfmMatrix.m' not found. You will need that file for TOPUP-related b-vector correction. Press key to continue..."
fi
if [ ! -f ${tmpltdir}/template_gICA.fsf ] ; then
read -p "WARNING: MELODIC template file not found. You may need to create that file..."
fi
fi
# are all subjects registered in struc. and func. infofiles ?
errpause=0
# ...in func. infofiles
for infofile in config_bet_magn config_unwarp_bold config_func2highres.reg ; do
for subj in `cat $subjdir/subjects` ; do
if [ $infofile = "config_func2highres.reg" ] ; then
for sess in `cat $subjdir/$subj/sessions_func` ; do
line=$(cat $subjdir/$infofile | awk '{print $1}' | grep -nx $(subjsess) || true)
if [ "x$line" = "x" ] ; then
errpause=1
echo "WARNING : '$infofile' : entry for '$(subjsess)' not found ! This may or may not be a problem depending on your setup."
if [ "$(cat ${subjdir}/${subj}/sessions_struc)" = "." ] ; then
read -p "Press key to add default value."
echo "$(subjsess) ." | tee -a ${subjdir}/$infofile
fi
fi
done
fi
line=$(cat $subjdir/$infofile | awk '{print $1}' | grep -nx ${subj} || true)
if [ "x$line" = "x" ] ; then
for sess in `cat $subjdir/$subj/sessions_func` ; do
line=$(cat $subjdir/$infofile | awk '{print $1}' | grep -nx $(subjsess) || true)
if [ "x$line" = "x" ] ; then
errpause=1
echo "WARNING : '$infofile' : entry for '$(subjsess)' not found ! This may or may not be a problem depending on your setup."
if [ $infofile = "config_bet_magn" ] ; then read -p "Press key to add default value." ; echo "$(subjsess) $BETMAGN_INFO" | tee -a ${subjdir}/$infofile ; fi
if [ $infofile = "config_unwarp_bold" ] ; then read -p "Press key to add default value." ; echo "$(subjsess) $DWIUNWARP_INFO" | tee -a ${subjdir}/$infofile ; fi
fi
done
fi
done
sort ${subjdir}/$infofile | uniq > $tmpdir/_${infofile} ; mv $tmpdir/_${infofile} ${subjdir}/$infofile
done
# ...in struc. infofiles
for infofile in config_bet_magn config_bet_lowb config_bet_struc0 config_bet_struc1 config_unwarp_dwi ; do
for subj in `cat $subjdir/subjects` ; do
line=$(cat $subjdir/$infofile | awk '{print $1}' | grep -nx ${subj} || true)
if [ "x$line" = "x" ] ; then
for sess in `cat $subjdir/$subj/sessions_struc` ; do
line=$(cat $subjdir/$infofile | awk '{print $1}' | grep -nx $(subjsess) || true)
if [ "x$line" = "x" ] ; then
errpause=1
echo "WARNING : '$infofile' : entry for '$(subjsess)' not found ! This may or may not be a problem depending on your setup."
if [ $infofile = "config_bet_magn" ] ; then read -p "Press key to add default value." ; echo "$(subjsess) $BETMAGN_INFO" | tee -a ${subjdir}/$infofile ; fi
if [ $infofile = "config_bet_lowb" ] ; then read -p "Press key to add default value." ; echo "$(subjsess) $BETLOWB_INFO" | tee -a ${subjdir}/$infofile ; fi
if [ $infofile = "config_bet_struc0" ] ; then read -p "Press key to add default value." ; echo "$(subjsess) $BETSTRUC0_INFO" | tee -a ${subjdir}/$infofile ; fi
if [ $infofile = "config_bet_struc1" ] ; then read -p "Press key to add default value." ; echo "$(subjsess) $BETSTRUC1_INFO" | tee -a ${subjdir}/$infofile ; fi
if [ $infofile = "config_unwarp_dwi" ] ; then read -p "Press key to add default value." ; echo "$(subjsess) $DWIUNWARP_INFO" | tee -a ${subjdir}/$infofile ; fi
fi
done
fi
done
sort ${subjdir}/$infofile | uniq > $tmpdir/_${infofile} ; mv $tmpdir/_${infofile} ${subjdir}/$infofile
done
if [ $errpause -eq 1 ] ; then echo "" ; echo "***CHECK*** (sleeping 2 seconds)..." ; sleep 2 ; echo "" ; fi
# list input files for each subject and session
checklist=""
if [ ! "x$pttrn_diffs" = "x" ] ; then checklist=$checklist" "$pttrn_diffs ; else checklist=$checklist" "0 ; fi
if [ ! "x$pttrn_bvals" = "x" ] ; then checklist=$checklist" "$pttrn_bvals ; else checklist=$checklist" "0 ; fi
if [ ! "x$pttrn_bvecs" = "x" ] ; then checklist=$checklist" "$pttrn_bvecs ; else checklist=$checklist" "0 ; fi
if [ ! "x$pttrn_strucs" = "x" ] ; then checklist=$checklist" "$pttrn_strucs ; else checklist=$checklist" "0 ; fi
if [ ! "x$pttrn_fmaps" = "x" ] ; then checklist=$checklist" "$pttrn_fmaps ; else checklist=$checklist" "0 ; fi
if [ ! "x$pttrn_bolds" = "x" ] ; then checklist=$checklist" "$pttrn_bolds ; else checklist=$checklist" "0 ; fi
# header line
for subj in `cat $subjdir/subjects` ; do
for sess in `cat $subjdir/$subj/sessions_* | sort | uniq` ; do
nchars=`printf "%3i subj %s , sess %s :" 1 $subj $sess`
nchars=${#nchars}
break
done
done
printf "%${nchars}s DWI BVAL BVEC STRC FMAP BOLD \n"
# cycle through...
n=1
for subj in `cat $subjdir/subjects` ; do
for sess in `cat $subjdir/$subj/sessions_* | sort | uniq` ; do
out=""
for i in $checklist ; do
if [ $i = "0" ] ; then
out=$out" "0
else
out=$out" "$(ls $srcdir/$subj/$sess/$i 2>/dev/null | wc -l)
fi
done
printf "%3i subj %s , sess %s :%s \n" $n $subj $sess "$out"
n=$[$n+1]
done
done
# display selected modules
echo "" ; echo "1ST LEVEL processing streams selected:"
echo -n "--- Scratch : " ; [ $SCRATCH = 1 ] && echo -n "SCRATCH " ; echo ""
echo -n "--- FMAP : " ; [ $FIELDMAP_STG1 = 1 ] && echo -n "STG1 " ; [ $FIELDMAP_STG2 = 1 ] && echo -n "STG2 " ; echo ""
echo -n "--- TOPUP : " ; [ $TOPUP_STG1 = 1 ] && echo -n "STG1 " ; [ $TOPUP_STG2 = 1 ] && echo -n "STG2 " ; [ $TOPUP_STG3 = 1 ] && echo -n "STG3 " ; [ $TOPUP_STG4 = 1 ] && echo -n "STG4 " ; [ $TOPUP_STG5 = 1 ] && echo -n "STG5 " ; [ $TOPUP_STG6 = 1 ] && echo -n "STG6 " ; echo ""
echo -n "--- FDT : " ; [ $FDT_STG1 = 1 ] && echo -n "STG1 " ; [ $FDT_STG2 = 1 ] && echo -n "STG2 " ; [ $FDT_STG3 = 1 ] && echo -n "STG3 " ; [ $FDT_STG4 = 1 ] && echo -n "STG4 " ; echo ""
echo -n "--- BPX : " ; [ $BPX_STG1 = 1 ] && echo -n "STG1 " ; echo ""
echo -n "--- RECON-ALL : " ; [ $RECON_STG1 = 1 ] && echo -n "STG1 " ; [ $RECON_STG2 = 1 ] && echo -n "STG2 " ; [ $RECON_STG3 = 1 ] && echo -n "STG3 " ; [ $RECON_STG4 = 1 ] && echo -n "STG4 " ; [ $RECON_STG5 = 1 ] && echo -n "STG5 " ; echo ""
echo -n "--- VBM : " ; [ $VBM_STG1 = 1 ] && echo -n "STG1 " ; [ $VBM_STG2 = 1 ] && echo -n "STG2 " ; [ $VBM_STG3 = 1 ] && echo -n "STG3 " ; [ $VBM_STG4 = 1 ] && echo -n "STG4 " ; [ $VBM_STG5 = 1 ] && echo -n "STG5 " ; echo ""
echo -n "--- TRACULA : " ; [ $TRACULA_STG1 = 1 ] && echo -n "STG1 " ; [ $TRACULA_STG2 = 1 ] && echo -n "STG2 " ; [ $TRACULA_STG3 = 1 ] && echo -n "STG3 " ; [ $TRACULA_STG4 = 1 ] && echo -n "STG4 " ; echo ""
echo -n "--- AUTOPTX : " ; [ $AUTOPTX_STG1 = 1 ] && echo -n "STG1 " ; echo ""
echo -n "--- BOLD : " ; [ $BOLD_STG1 = 1 ] && echo -n "STG1 " ; [ $BOLD_STG2 = 1 ] && echo -n "STG2 " ; [ $BOLD_STG3 = 1 ] && echo -n "STG3 " ; [ $BOLD_STG4 = 1 ] && echo -n "STG4 " ; [ $BOLD_STG5 = 1 ] && echo -n "STG5 " ; echo ""
echo -n "--- ALFF : " ; [ $ALFF_STG1 = 1 ] && echo -n "STG1 " ; [ $ALFF_STG2 = 1 ] && echo -n "STG2 " ; [ $ALFF_STG3 = 1 ] && echo -n "STG3 " ; echo ""
echo "2ND LEVEL processing streams selected:"
echo -n "--- TBSS : " ; [ $TBSS_STG1 = 1 ] && echo -n "STG1 " ; [ $TBSS_STG2 = 1 ] && echo -n "STG2 " ; [ $TBSS_STG3 = 1 ] && echo -n "STG3 " ; [ $TBSS_STG4 = 1 ] && echo -n "STG4 " ; [ $TBSS_STG5 = 1 ] && echo -n "STG5 " ; echo ""
echo -n "--- FS_STATS : " ; [ $FS_STATS_STG1 = 1 ] && echo -n "STG1 " ; [ $FS_STATS_STG2 = 1 ] && echo -n "STG2 " ; [ $FS_STATS_STG3 = 1 ] && echo -n "STG3 " ; [ $FS_STATS_STG4 = 1 ] && echo -n "STG4 " ; echo ""
echo -n "--- VBM_2NDLEV : " ; [ $VBM_2NDLEV_STG1 = 1 ] && echo -n "STG1 " ; [ $VBM_2NDLEV_STG2 = 1 ] && echo -n "STG2 " ; [ $VBM_2NDLEV_STG3 = 1 ] && echo -n "STG3 " ; echo ""
echo -n "--- MELODIC_2NDLEV : " ; [ $MELODIC_2NDLEV_STG1 = 1 ] && echo -n "STG1 " ; [ $MELODIC_2NDLEV_STG2 = 1 ] && echo -n "STG2 " ; echo ""
echo -n "--- MELODIC_CMD : " ; [ $MELODIC_CMD_STG1 = 1 ] && echo -n "STG1 " ; echo ""
echo -n "--- DUALREG : " ; [ $DUALREG_STG1 = 1 ] && echo -n "STG1 " ; [ $DUALREG_STG2 = 1 ] && echo -n "STG2 " ; echo ""
echo -n "--- FSLNETS : " ; [ $FSLNETS_STG1 = 1 ] && echo -n "STG1 " ; echo ""
echo -n "--- ALFF_2NDLEV : " ; [ $ALFF_2NDLEV_STG1 = 1 ] && echo -n "STG1 " ; [ $ALFF_2NDLEV_STG2 = 1 ] && echo -n "STG2 " ; echo ""
echo ""
echo "***CHECK*** (sleeping 2 seconds)..."
sleep 2
# check SGE
if [ x"$SGE_ROOT" != "x" ] ; then
echo ""
qstat -f
echo ""
else
echo ""
echo "SGE_ROOT variable not set -> not using randomise_parallel."
RANDOMISE_PARALLEL=0
echo ""
fi
# check if source directory exists (where nifti originals are located)
if [ ! -d $srcdir ] ; then
echo "ERROR: '$srcdir' (where nifti originals should be located) does not exist - creating it and exiting..."
for subj in `cat $subjdir/subjects`; do
for sess in `cat $subjdir/$subj/sessions_struc` ; do
mkdir -p $srcdir/$subj/$sess
done
done
exit 1
fi
# dos2unix bval/bvec textfiles (just in case...)
echo "Ensuring UNIX line endings in bval-/bvec textfiles..."
err=0
for subj in `cat $subjdir/subjects` ; do
for sess in `cat $subjdir/$subj/sessions_struc` ; do
dwi_txtfiles=""
if [ x${pttrn_diffspuls} != "x" ] ; then
if [ x${pttrn_bvalsplus} != "x" ] ; then dwi_txtfiles=$dwi_txtfiles" "$srcdir/$subj/$sess/$pttrn_bvalsplus ; fi
if [ x${pttrn_bvalsminus} != "x" ] ; then dwi_txtfiles=$dwi_txtfiles" "$srcdir/$subj/$sess/$pttrn_bvalsminus ; fi
if [ x${pttrn_bvecsplus} != "x" ] ; then dwi_txtfiles=$dwi_txtfiles" "$srcdir/$subj/$sess/$pttrn_bvecsplus ; fi
if [ x${pttrn_bvecsminus} != "x" ] ; then dwi_txtfiles=$dwi_txtfiles" "$srcdir/$subj/$sess/$pttrn_bvecsminus ; fi
fi
if [ x${pttrn_diffs} != "x" ] ; then
if [ x${pttrn_bvals} != "x" ] ; then dwi_txtfiles=$dwi_txtfiles" "$srcdir/$subj/$sess/$pttrn_bvals ; fi
if [ x${pttrn_bvecs} != "x" ] ; then dwi_txtfiles=$dwi_txtfiles" "$srcdir/$subj/$sess/$pttrn_bvecs ; fi
fi
dwi_txtfiles=$(echo $dwi_txtfiles| row2col | sort | uniq)
for i in $dwi_txtfiles ; do
#echo " $i"
if [ $(ls $i | wc -l) -eq 0 ] ; then echo "ERROR: 'ls $i' is empty." ; err=1 ; continue ; fi
if [ $(ls $i | wc -l) -gt 1 ] ; then echo "ERROR: 'ls $i' is ambiguous (more than one result)." ; err=1 ; continue ; fi
dos2unix -q $i
done
done
done
if [ $err -eq 1 ] ; then echo "An ERROR has occured - exiting..." ; exit 1 ; fi
echo "...done." ; echo ""
# check bvals, bvecs and diff. files for consistent number of entries
if [ $CHECK_CONSISTENCY_DIFFS = 1 ] ; then
if [ x${pttrn_bvals} != "x" -a x${pttrn_bvecs} != "x" -a x${pttrn_diffs} != "x" ] ; then
echo "Checking bvals/bvecs- and DWI files for consistent number of entries..."
for subj in `cat $subjdir/subjects` ; do
for sess in `cat $subjdir/$subj/sessions_struc` ; do
fldr=$srcdir/$subj/$sess/
echo -n "subj $subj , sess $sess : "
checkConsistency "$fldr/$pttrn_diffs" "$fldr/$pttrn_bvals" "$fldr/$pttrn_bvecs"
done
done
echo ""
fi
fi
# Updating MELODIC templates
echo "Copying ICA templates..."
mkdir -p $gicadir/templates.gica/groupmelodic.ica
cp $(dirname $scriptdir)/fsl/templates/rsn* $gicadir/templates.gica/groupmelodic.ica/
echo "...done." ; echo ""
# make log directory for fsl_sub
mkdir -p $logdir
$scriptdir/delbrokenlinks.sh $logdir 1 # delete broken symlinks
# make directory for 2nd level GLMs
mkdir -p $glmdir_tbss
mkdir -p $glmdir_vbm
# create freesurfer subjects dir
for subj in `cat $subjdir/subjects`; do
for sess in `cat $subjdir/$subj/sessions_struc` ; do
mkdir -p $FS_subjdir/$(subjsess)
done
done
# create freesurfer sessions dir
for subj in `cat $subjdir/subjects`; do
for sess in `cat $subjdir/$subj/sessions_func` ; do
mkdir -p $FS_sessdir/$(subjsess)
done
done
# wait until cluster is ready...
waitIfBusy
# change to subjects directory...
cd $subjdir
echo ""
###########################
# ----- BEGIN SCRATCH -----
###########################
if [ $SCRATCH -eq 1 ]; then
echo "----- BEGIN SCRATCH -----"
exit
fi
#########################
# ----- END SCRATCH -----
#########################
waitIfBusy
############################
# ----- BEGIN FIELDMAP -----
############################
# FIELDMAP prepare
if [ $FIELDMAP_STG1 -eq 1 ]; then
echo "----- BEGIN FIELDMAP_STG1 -----"
for subj in `cat $subjdir/subjects` ; do
for sess in `cat $subjdir/$subj/sessions_* | sort | uniq` ; do
if [ $(ls ${srcdir}/${subj}/${sess}/${pttrn_fmaps} 2>/dev/null | wc -l) -eq 0 ] ; then echo "FIELDMAP : subj $subj , sess $sess : no fieldmap found - continuing..." ; continue ; fi
fldr=$subjdir/${subj}/${sess}/fm
# create fieldmap directory
mkdir -p $fldr
# find magnitude
fm_m=`ls ${srcdir}/${subj}/${sess}/${pttrn_fmaps} | sed -n 1p` # first in listing is magnitude (last is phase-difference volume) (!)
imcp $fm_m $fldr
# split magnitude
echo "FIELDMAP : subj $subj , sess $sess : extracting magnitude image ${fm_m}..."
fslroi $fm_m ${fldr}/magn 0 1 # extract first of the two magnitude images, do not fsl_sub (!)
#fslmaths $fm_m -Tmean ${fldr}/magn # the mean has better SNR
# betting magnitude (with variable FI thresholds)
for f in 0.50 0.40 0.30 ; do
echo "FIELDMAP : subj $subj , sess $sess : betting magnitude image with fi=${f}..."
fsl_sub -l $logdir -N fm_bet_$(subjsess) bet ${fldr}/magn ${fldr}/magn_brain_${f} -m -f $f
done
done
done
fi
waitIfBusy
# FIELDMAP create
if [ $FIELDMAP_STG2 -eq 1 ]; then
echo "----- BEGIN FIELDMAP_STG2 -----"
for subj in `cat $subjdir/subjects` ; do
for sess in `cat $subjdir/$subj/sessions_* | sort | uniq` ; do
if [ $(ls ${srcdir}/${subj}/${sess}/${pttrn_fmaps} 2>/dev/null | wc -l) -eq 0 ] ; then echo "FIELDMAP : subj $subj , sess $sess : no fieldmap found - continuing..." ; continue ; fi
fldr=$subjdir/${subj}/${sess}/fm
# get bet threshold
f=`getBetThres ${subjdir}/config_bet_magn $subj $sess`
# bet, if necessary
if [ $f = "mod" ] ; then
if [ ! -f ${fldr}/magn_brain_${f}.nii.gz -o ! -f ${fldr}/magn_brain_${f}_mask.nii.gz ] ; then
echo "FIELDMAP : subj $subj , sess $sess : ERROR : externally modified volume (magn_brain_${f}.nii.gz) & mask (magn_brain_${f}_mask.nii.gz) not found - exiting..." ; exit 1
fi
else
echo "FIELDMAP : subj $subj , sess $sess : betted magnitude image with fi=${f}..."
bet ${fldr}/magn ${fldr}/magn_brain_${f} -m -f $f
fi
# find phase image
fm_p=`ls ${srcdir}/${subj}/${sess}/${pttrn_fmaps} | tail -n 1` # last in list is phase image, check pattern (!)
# copy files to fieldmap folder
imcp $fm_p $fldr
echo "FIELDMAP : subj $subj , sess $sess : using magn_brain_${f}_mask"
imcp $fldr/magn_brain_${f} $fldr/magn_brain
imcp $fldr/magn_brain_${f}_mask $fldr/magn_brain_mask
# define stats for the phase image
range=`fslstats $fm_p -R`
min=`echo $range | cut -d " " -f1`
max=`echo $range | cut -d " " -f2`
add=$(echo "-($min + $max)/2" | bc -l)
div=$(echo "$max + $add" | bc -l)
# display info
printf "FIELDMAP : subj $subj , sess $sess : phase image $fm_p - info: min: %.2f max: %.2f add: %.2f div: %.2f pi: %.5f \n" $min $max $add $div $PI
# erode by one voxel (default kernel 3x3x3)
echo "FIELDMAP : subj $subj , sess $sess : eroding brain mask a bit..."
fslmaths $fldr/magn_brain_${f}_mask -ero $fldr/magn_brain_mask_ero
# scale to -pi ... +pi
fslmaths $fm_p -add $add -div $div -mul $PI $fldr/phase_rad -odt float
echo "FIELDMAP : subj $subj , sess $sess : phase image is scaled to `fslstats $fldr/phase_rad -R`"
# unwrap
echo "FIELDMAP : subj $subj , sess $sess : unwrapping phase image..."
prelude -p $fldr/phase_rad -m $fldr/magn_brain_mask_ero -a $fldr/magn_brain_${f} -o $fldr/uphase_rad
# divide by echo time difference
echo "FIELDMAP : subj $subj , sess $sess : normalizing phase image to dTE (${deltaTEphase}) and centering to median (P50)..."
fslmaths $fldr/uphase_rad -div $deltaTEphase $fldr/fmap_rads
# center to median
p50=`fslstats $fldr/fmap_rads -k $fldr/magn_brain_mask_ero -P 50`
echo "FIELDMAP : subj $subj , sess $sess : P50: $p50"
fslmaths $fldr/fmap_rads -sub $p50 -mas $fldr/magn_brain_mask_ero $fldr/fmap_rads_masked
# jetzt noch swi ohne swi:
# smooth with gauss kernel of s=xx mm and subtract to get filtered image
fslmaths $fldr/uphase_rad -s 10 $fldr/uphase_rad_s10
fslmaths $fldr/uphase_rad -sub $fldr/uphase_rad_s10 $fldr/uphase_rad_filt
# center pSWI to median
p50=`fslstats $fldr/uphase_rad_filt -k $fldr/magn_brain_mask_ero -P 50`
echo "FIELDMAP : subj $subj , sess $sess : pSWI: P50: $p50"
fslmaths $fldr/uphase_rad_filt -sub $p50 -mas $fldr/magn_brain_mask_ero $fldr/uphase_rad_filt_masked
done
done
fi
##########################
# ----- END FIELDMAP -----
##########################
waitIfBusy
#########################
# ----- BEGIN TOPUP -----
#########################
# TOPUP prepare
if [ $TOPUP_STG1 -eq 1 ] ; then
echo "----- BEGIN TOPUP_STG1 -----"
# check bvals, bvecs and dwi files for consistent number of entries
errflag=0
echo "TOPUP : Checking bvals/bvecs- and DWI files for consistent number of entries..."
for subj in `cat subjects` ; do
for sess in `cat ${subj}/sessions_struc` ; do
fldr=$srcdir/$subj/$sess
i=1
for dwi_p in $(ls $fldr/$pttrn_diffsplus) ; do
dwi_m=$(ls $fldr/$pttrn_diffsminus | sed -n ${i}p)
n_bvalsplus=`ls $fldr/$pttrn_bvalsplus | sed -n ${i}p | xargs cat | wc -w` ; n_bvecsplus=`ls $fldr/$pttrn_bvecsplus | sed -n ${i}p | xargs cat | wc -w`
n_bvalsminus=`ls $fldr/$pttrn_bvalsminus | sed -n ${i}p | xargs cat | wc -w` ; n_bvecsminus=`ls $fldr/$pttrn_bvecsminus | sed -n ${i}p | xargs cat | wc -w`
nvolplus=`countVols "$dwi_p"` ; nvolminus=`countVols "$dwi_m"`
if [ $n_bvalsplus -eq $nvolplus -a $n_bvecsplus=$(echo "scale=0 ; 3*$n_bvalsplus" | bc -l) ] ; then
echo "TOPUP : subj $subj , sess $sess : $(basename $dwi_p) : consistent number of entries in bval/bvec/dwi files ($n_bvalsplus)"
else
echo "TOPUP : subj $subj , sess $sess : $(basename $dwi_p) : ERROR : inconsistent number of entries in bval:$n_bvalsplus / bvec:$(echo "scale=0; $n_bvecsplus/3" | bc -l) / dwi:$nvolplus" ; errflag=1
fi
if [ $n_bvalsminus -eq $nvolminus -a $n_bvecsminus=$(echo "scale=0 ; 3*$n_bvalsminus" | bc -l) ] ; then
echo "TOPUP : subj $subj , sess $sess : $(basename $dwi_m) : consistent number of entries in bval/bvec/dwi files ($n_bvalsminus)"
else
echo "TOPUP : subj $subj , sess $sess : $(basename $dwi_m) : ERROR : inconsistent number of entries in bval:$n_bvalsminus / bvec:$(echo "scale=0; $n_bvecsminus/3" | bc -l) / dwi:$nvolminus" ; errflag=1
fi
if [ $n_bvalsplus -eq $n_bvalsminus ] ; then
echo "TOPUP : subj $subj , sess $sess : blip(+/-) : consistent number of entries ($n_bvalsminus)"
else
echo "TOPUP : subj $subj , sess $sess : blip(+/-) : ERROR : inconsistent number of entries (+: $n_bvalsplus -: $n_bvalsminus)" ; errflag=1
fi
i=$[$i+1]
done
done
done
if [ $errflag -eq 1 ] ; then echo "DWI consistency check : Exiting due to errors !" ; exit 1 ; fi
fldr="" ; n_bvalsplus="" ; n_bvalsminus="" ; n_bvecsplus="" ; n_bvecsminus="" ; nvolplus="" ; nvolminus="" ; errflag="" ; subj="" ; sess="" ; i="" ; dwi_m="" ; dwi_p=""
echo "TOPUP : ...done."
# end check
for subj in `cat subjects` ; do
for sess in `cat ${subj}/sessions_struc` ; do
# check if we have acquisition parameters
defineDWIparams $subjdir/config_acqparams_dwi $subj $sess
if [ "x$pttrn_diffsplus" = "x" -o "x$pttrn_diffsminus" = "x" -o "x$pttrn_bvalsplus" = "x" -o "x$pttrn_bvalsminus" = "x" -o "x$pttrn_bvecsplus" = "x" -o "x$pttrn_bvecsminus" = "x" ] ; then
echo "TOPUP : subj $subj , sess $sess : ERROR : file search pattern for blipUp/blipDown DWIs not set..."
continue
fi
fldr=${subjdir}/${subj}/${sess}/topup
mkdir -p $fldr
# display info
echo "TOPUP : subj $subj , sess $sess : preparing TOPUP... "
# are the +- diffusion files in equal number ?
n_plus=`ls $srcdir/$subj/$sess/$pttrn_diffsplus | wc -l`
n_minus=`ls $srcdir/$subj/$sess/$pttrn_diffsminus | wc -l`
if [ ! $n_plus -eq $n_minus ] ; then
echo "TOPUP : subj $subj , sess $sess : ERROR : number of +blips diff. files ($n_plus) != number of -blips diff. files ($n_minus) - continuing loop..."
continue
elif [ $n_plus -eq 0 -a $n_minus -eq 0 ] ; then
echo "TOPUP : subj $subj , sess $sess : ERROR : no blip-up/down diffusion files found for TOPUP (+/- must be part of the filename) - continuing loop..."
continue
fi
# count +/- bvec/bval-files
ls $srcdir/$subj/$sess/$pttrn_bvecsplus > $fldr/bvec+.files
ls $srcdir/$subj/$sess/$pttrn_bvecsminus > $fldr/bvec-.files
cat $fldr/bvec-.files $fldr/bvec+.files > $fldr/bvec.files
ls $srcdir/$subj/$sess/$pttrn_bvalsplus > $fldr/bval+.files
ls $srcdir/$subj/$sess/$pttrn_bvalsminus > $fldr/bval-.files
cat $fldr/bval-.files $fldr/bval+.files > $fldr/bval.files
n_vec_plus=`cat $fldr/bvec+.files | wc -l`
n_vec_minus=`cat $fldr/bvec-.files | wc -l`
n_val_plus=`cat $fldr/bval+.files | wc -l`
n_val_minus=`cat $fldr/bval-.files | wc -l`
# are the +/- bvec-files equal in number ?
if [ ! $n_vec_plus -eq $n_vec_minus ] ; then
echo "TOPUP : subj $subj , sess $sess : ERROR : number of +blips bvec-files ($n_vec_plus) != number of -blips bvec-files ($n_vec_minus) - continuing loop..."
continue
elif [ $n_vec_plus -eq 0 -a $n_vec_minus -eq 0 ] ; then
echo "TOPUP : subj $subj , sess $sess : ERROR : no blip-up/down bvec-files found for TOPUP (+/- must be part of the filename) - continuing loop..."
continue
fi
# are the +/- bval-files equal in number ?
if [ ! $n_val_plus -eq $n_val_minus ] ; then
echo "TOPUP : subj $subj , sess $sess : ERROR : number of +blips bval-files ($n_val_plus) != number of -blips bval-files ($n_val_minus) - continuing loop..."
continue
elif [ $n_val_plus -eq 0 -a $n_val_minus -eq 0 ] ; then
echo "TOPUP : subj $subj , sess $sess : ERROR : no blip-up/down bval-files found for TOPUP (+/- must be part of the filename) - continuing loop..."
continue
fi
# concatenate +bvecs and -bvecs
concat_bvals $srcdir/$subj/$sess/"$pttrn_bvalsminus" $fldr/bvals-_concat.txt
concat_bvals $srcdir/$subj/$sess/"$pttrn_bvalsplus" $fldr/bvals+_concat.txt
concat_bvecs $srcdir/$subj/$sess/"$pttrn_bvecsminus" $fldr/bvecs-_concat.txt
concat_bvecs $srcdir/$subj/$sess/"$pttrn_bvecsplus" $fldr/bvecs+_concat.txt
nbvalsplus=$(wc -w $fldr/bvals+_concat.txt | cut -d " " -f 1)
nbvalsminus=$(wc -w $fldr/bvals-_concat.txt | cut -d " " -f 1)
nbvecsplus=$(wc -w $fldr/bvecs+_concat.txt | cut -d " " -f 1)
nbvecsminus=$(wc -w $fldr/bvecs-_concat.txt | cut -d " " -f 1)
# check number of entries in concatenated bvals/bvecs files
n_entries=`countVols $srcdir/$subj/$sess/"$pttrn_diffsplus"`
if [ $nbvalsplus = $nbvalsminus -a $nbvalsplus = $n_entries -a $nbvecsplus = `echo "3*$n_entries" | bc` -a $nbvecsplus = $nbvecsminus ] ; then
echo "TOPUP : subj $subj , sess $sess : number of entries in bvals- and bvecs files consistent ($n_entries entries)."
else
echo "TOPUP : subj $subj , sess $sess : ERROR : number of entries in bvals- and bvecs files NOT consistent - continuing loop..."
echo "(diffs+: $n_entries ; bvals+: $nbvalsplus ; bvals-: $nbvalsminus ; bvecs+: $nbvecsplus /3 ; bvecs-: $nbvecsminus /3)"
continue
fi
# check if +/- bval entries are the same
i=1
for bval in `cat $fldr/bvals+_concat.txt` ; do
if [ $bval != $(cat $fldr/bvals-_concat.txt | cut -d " " -f $i) ] ; then
echo "TOPUP : subj $subj , sess $sess : ERROR : +bval entries do not match -bval entries (they should have the same values !) - exiting..."
exit
fi
i=$[$i+1]
done
# getting unwarp direction
uw_dir=`getUnwarpDir ${subjdir}/config_unwarp_dwi $subj $sess`
echo "TOPUP : subj $subj , sess $sess : unwarp direction is '$uw_dir'."
x=0 ; y=0 ; z=0;
if [ "$uw_dir" = "+x" ] ; then x=1 ; fi
if [ "$uw_dir" = "-x" ] ; then x=-1 ; fi
if [ "$uw_dir" = "+y" ] ; then y=-1 ; fi # sic! (so that TOPUP and SIEMENS phasemaps match in sign)
if [ "$uw_dir" = "-y" ] ; then y=1 ; fi # sic! (so that TOPUP and SIEMENS phasemaps match in sign)
if [ "$uw_dir" = "+z" ] ; then z=1 ; fi
if [ "$uw_dir" = "-z" ] ; then z=-1 ; fi
mx=$(echo "scale=0; -1 * ${x}" | bc -l)
my=$(echo "scale=0; -1 * ${y}" | bc -l)
mz=$(echo "scale=0; -1 * ${z}" | bc -l)
blipdownline="$mx $my $mz $TROT_topup"
blipupline="$x $y $z $TROT_topup"
# display info
echo "TOPUP : subj $subj , sess $sess : example blip-down line:"
echo " $blipdownline"
echo "TOPUP : subj $subj , sess $sess : example blip-up line:"
echo " $blipupline"
# creating index file for TOPUP
echo "TOPUP : subj $subj , sess $sess : creating index file for TOPUP..."
rm -f $fldr/$(subjsess)_acqparam.txt ; rm -f $fldr/$(subjsess)_acqparam_inv.txt ; rm -f $fldr/diff.files # clean-up previous runs...
diffsminus=`ls ${srcdir}/${subj}/${sess}/${pttrn_diffsminus}`
for file in $diffsminus ; do
nvol=`fslinfo $file | grep ^dim4 | awk '{print $2}'`
echo "$file n:${nvol}" | tee -a $fldr/diff.files
for i in `seq 1 $nvol`; do
echo "$blipdownline" >> $fldr/$(subjsess)_acqparam.txt
echo "$blipupline" >> $fldr/$(subjsess)_acqparam_inv.txt
done
done
diffsplus=`ls ${srcdir}/${subj}/${sess}/${pttrn_diffsplus}`
for file in $diffsplus ; do
nvol=`fslinfo $file | grep ^dim4 | awk '{print $2}'`
echo "$file n:${nvol}" | tee -a $fldr/diff.files
for i in `seq 1 $nvol`; do
echo "$blipupline" >> $fldr/$(subjsess)_acqparam.txt
echo "$blipdownline" >> $fldr/$(subjsess)_acqparam_inv.txt
done
done
# merging diffusion images for TOPUP
echo "TOPUP : subj $subj , sess $sess : merging diffs... "
fsl_sub -l $logdir -N topup_fslmerge_$(subjsess) fslmerge -t $fldr/diffs_merged $(cat $fldr/diff.files | cut -d " " -f 1)
done
done
waitIfBusy
# perform eddy-correction, if applicable
if [ $TOPUP_USE_EC -eq 1 ] ; then
for subj in `cat subjects` ; do
for sess in `cat ${subj}/sessions_struc` ; do
fldr=${subjdir}/${subj}/${sess}/topup
# cleanup previous runs...
rm -f $fldr/ec_diffs_merged_???_*.nii.gz # removing temporary files from prev. run
if [ ! -z "$(ls $fldr/ec_diffs_merged_???.ecclog 2>/dev/null)" ] ; then
echo "TOPUP : subj $subj , sess $sess : WARNING : eddy_correct logfile(s) from a previous run detected - deleting..."
rm $fldr/ec_diffs_merged_???.ecclog # (!)
fi
# eddy-correct each run...
for i in `seq -f %03g 001 $(cat $fldr/diff.files | wc -l)` ; do # note: don't use seq -w (bash compatibility issues!) (!)
dwifile=$(cat $fldr/diff.files | sed -n ${i}p | cut -d " " -f 1)
bvalfile=$(cat $fldr/bval.files | sed -n ${i}p)
# get B0 index
b0img=`getB0Index $bvalfile $fldr/ec_ref_${i}.idx | cut -d " " -f 1` ; min=`getB0Index $bvalfile $fldr/ec_ref_${i}.idx | cut -d " " -f 2`
# create a task file for fsl_sub, which is needed to avoid accumulations when SGE does a re-run on error
echo "rm -f $fldr/ec_diffs_merged_${i}*.nii.gz ; \
rm -f $fldr/ec_diffs_merged_${i}.ecclog ; \
$scriptdir/eddy_correct.sh $dwifile $fldr/ec_diffs_merged_${i} $b0img $TOPUP_EC_DOF $TOPUP_EC_COST trilinear" > $fldr/topup_ec_${i}.cmd
# eddy-correct
echo "TOPUP : subj $subj , sess $sess : eddy_correction of '$dwifile' (ec_diffs_merged_${i}) is using volume no. $b0img as B0 (val:${min})..."
fsl_sub -l $logdir -N topup_eddy_correct_$(subjsess) -t $fldr/topup_ec_${i}.cmd
done
done
done
waitIfBusy
# plot ecclogs...
for subj in `cat subjects` ; do
for sess in `cat ${subj}/sessions_struc` ; do
fldr=${subjdir}/${subj}/${sess}/topup
cd $fldr
for i in `seq -f %03g 001 $(cat $fldr/diff.files | wc -l)` ; do # note: don't use seq -w (bash compatibility issues!) (!)
echo "TOPUP : subj $subj , sess $sess : plotting ec_diffs_merged_${i}.ecclog..."
eddy_correct_plot ec_diffs_merged_${i}.ecclog $(subjsess)-${i}
# horzcat
pngappend ec_disp.png + ec_rot.png + ec_trans.png ec_${i}.png
# accumulate
if [ $i -gt 1 ] ; then
pngappend ec_plot.png - ec_${i}.png ec_plot.png
else
cp ec_${i}.png ec_plot.png
fi
# cleanup
rm ec_disp.png ec_rot.png ec_trans.png ec_${i}.png
done
cd $subjdir
done
done
fi
fi
waitIfBusy
# TOPUP low-B images: create index and extract
if [ $TOPUP_STG2 -eq 1 ] ; then
echo "----- BEGIN TOPUP_STG2 -----"
for subj in `cat subjects` ; do
for sess in `cat ${subj}/sessions_struc` ; do
fldr=${subjdir}/${subj}/${sess}/topup
if [ ! -f $fldr/$(subjsess)_acqparam.txt ] ; then echo "TOPUP : subj $subj , sess $sess : ERROR : parameter file $fldr/$(subjsess)_acqparam.txt not found - continuing loop..." ; continue ; fi
# display info
echo "TOPUP : subj $subj , sess $sess : concatenate bvals and bvecs... "
echo "`cat $fldr/bvals-_concat.txt`" "`cat $fldr/bvals+_concat.txt`" > $fldr/bvals_concat.txt
paste -d " " $fldr/bvecs-_concat.txt $fldr/bvecs+_concat.txt > $fldr/bvecs_concat.txt
# get B0 index
min=`row2col $fldr/bvals_concat.txt | getMin` # find minimum value (usually representing the "B0" image)
echo "TOPUP : subj $subj , sess $sess : minimum b-value in merged diff. is $min"
b0idces=`getIdx $fldr/bvals_concat.txt $min`
echo $b0idces | row2col > $fldr/lowb.idx
# creating index file for topup (only low-B images)
echo "TOPUP : subj $subj , sess $sess : creating index file for TOPUP (only low-B images)..."
rm -f $fldr/$(subjsess)_acqparam_lowb.txt ; rm -f $fldr/$(subjsess)_acqparam_lowb_inv.txt # clean-up previous runs...
for b0idx in $b0idces ; do
line=`echo "$b0idx + 1" | bc -l`
cat $fldr/$(subjsess)_acqparam.txt | sed -n ${line}p >> $fldr/$(subjsess)_acqparam_lowb.txt
cat $fldr/$(subjsess)_acqparam_inv.txt | sed -n ${line}p >> $fldr/$(subjsess)_acqparam_lowb_inv.txt
done
# extract B0 images
lowbs=""
for b0idx in $b0idces ; do
echo "TOPUP : subj $subj , sess $sess : found B0 image in merged diff. at pos. $b0idx (val:${min}) - extracting..."
lowb="$fldr/b${min}_`printf '%05i' $b0idx`"
fsl_sub -l $logdir -N topup_fslroi_$(subjsess) fslroi $fldr/diffs_merged $lowb $b0idx 1
lowbs=$lowbs" "$lowb
done
# save filenames to text file
echo "$lowbs" > $fldr/lowb.files; lowbs=""
# wait here to prevent overload...
waitIfBusy
done
done
fi
waitIfBusy
# TOPUP merge B0 images
if [ $TOPUP_STG3 -eq 1 ] ; then
echo "----- BEGIN TOPUP_STG3 -----"
for subj in `cat subjects` ; do
for sess in `cat ${subj}/sessions_struc` ; do
fldr=${subjdir}/${subj}/${sess}/topup
if [ ! -f $fldr/$(subjsess)_acqparam.txt ] ; then echo "TOPUP : subj $subj , sess $sess : ERROR : parameter file $fldr/$(subjsess)_acqparam.txt not found - continuing loop..." ; continue ; fi
# merge B0 images
echo "TOPUP : subj $subj , sess $sess : merging low-B volumes..."
fsl_sub -l $logdir -N topup_fslmerge_$(subjsess) fslmerge -t $fldr/$(subjsess)_lowb_merged $(cat $fldr/lowb.files)
done
done
fi
waitIfBusy
# TOPUP execute TOPUP
if [ $TOPUP_STG4 -eq 1 ] ; then