# Settings file for FIX # Modify these settings based on your system setup FIXFEATUREVERSION=1.06 # Get the OS and CPU type FSL_FIX_OS=$(uname -s) FSL_FIX_ARCH=$(uname -m) if [ -z "${FSL_FIXDIR}" ]; then if [ "X$0" = "X-bash" ]; then FSL_FIXDIR=$(pwd) else FSL_FIXDIR=$( cd "$(dirname "$0")" ; pwd) fi export FSL_FIXDIR fi FIXVERSION=`cat $FSL_FIXDIR/fixversion` # Disable errexit so that which commands can't cause abort cur_errexit=$(set -o | grep "errexit" | awk '{ print $2 }') if [ "${cur_errexit}" = "on" ]; then set +o errexit fi # edit the following variables according to your local setup # Part I MATLAB/Octave mode # ========================= # This variable selects how we run the MATLAB portions of FIX. # It takes the values 0-2: # 0 - Try running the compiled version of the function # 1 - Use the MATLAB script version # 2 - Use Octave script version if [ -z "${FSL_FIX_MATLAB_MODE}" ]; then FSL_FIX_MATLAB_MODE=0 fi # Part IIa MATLAB compiled version # ================================ if [ "$FSL_FIX_MATLAB_MODE" -eq 0 ]; then # Point this variable at the folder containing an installed MATLAB compiler runtime. # e.g. /usr/local/mcr # Within this folder must be the versioned runtimes, e.g. v93 etc if [ -z "${FSL_FIX_MCRROOT}" ]; then FSL_FIX_MCRROOT="/usr/local/MATLAB/MCR" if [ ! -x "$FSL_FIX_MCRROOT" ]; then echo "Can't find the MATLAB compiler runtime, please set FSL_FIX_MCRROOT in the settings.sh file." >2 fi fi # The following variables should not need changing # This is name of the folder containing the compiled MATLAB functions if [ -z "${FSL_FIX_MLCDIR}" ]; then FSL_FIX_MLCDIR="${FSL_FIXDIR}/compiled/${FSL_FIX_OS}/${FSL_FIX_ARCH}" fi # This is the version of the runtime FIX has been compiled for if [ -z "${FSL_FIX_MCRV}" ]; then if [ -f "${FSL_FIX_MLCDIR}/MCR.version" ]; then FSL_FIX_MCRV=$(cat "${FSL_FIX_MLCDIR}/MCR.version") fi fi # This is where FIX will look for the compiler runtime if [ ! -z "${FSL_FIX_MCRV}" -a -z "${FSL_FIX_MCR}" ]; then FSL_FIX_MCR="${FSL_FIX_MCRROOT}/${FSL_FIX_MCRV}" fi fi # Part IIb MATLAB settings # ======================== # Skip this if you aren't using mode 1 if [ "$FSL_FIX_MATLAB_MODE" -eq 1 ]; then # Look for installed MATLAB if [ -z "${MATLAB_BIN}" ]; then MATLAB_BIN=$(which matlab 2>/dev/null) fi # Look for installed MCC - not needed if you aren't going to compile FIX if [ -z "${MCC_BIN}" ]; then MCC_BIN=$(which mcc 2>/dev/null) fi # Point this variable at your MATLAB command - this is usually $FSL_FIX_MATLAB_ROOT/bin/matlab if [ -z "${FSL_FIX_MATLAB}" ]; then FSL_FIX_MATLAB="${MATLAB_BIN}" fi if [ -z "${FSL_FIX_MATLAB}" ]; then echo "Please set FSL_FIX_MATLAB variable in the settings.sh file to point at your MATLAB program" >2 fi # Point this variable at your MATLAB install folder if [ -z "${FSL_FIX_MATLAB_ROOT}" ]; then FSL_FIX_MATLAB_ROOT="$(dirname "${FSL_FIX_MATLAB}")/.." # On OS X this will most likely be something like /Applications/MATLAB_R20XX.app fi # Point this variable at your MATLAB compiler command - this is usually $FSL_FIX_MATLAB_ROOT/bin/mcc # Not needed if you don't intend to compile FIX if [ -z "${FSL_FIX_MCC}" ]; then FSL_FIX_MCC="${MCC_BIN}" fi # The following variables should not need changing # This is name of the folder containing the compiled MATLAB functions if [ -z "${FSL_FIX_MLCDIR}" ]; then FSL_FIX_MLCDIR="${FSL_FIXDIR}/compiled/${FSL_FIX_OS}/${FSL_FIX_ARCH}" fi # See README for instructions on compilation of the MATLAB portions # Set this to the MATLAB start-up options. Typically you will # want to disable Java, display output, the desktop environment # and the splash screen if [ -z "${FSL_FIX_MLOPTS}" ]; then FSL_FIX_MLOPTS="-nojvm -nodisplay -nodesktop -nosplash" fi # Set this to the MATLAB 'evaluate string' option if [ -z "${FSL_FIX_MLEVAL}" ]; then FSL_FIX_MLEVAL="-r" fi # Set this to the pass in file option if [ -z "${FSL_FIX_MLFILE}" ]; then FSL_FIX_MLFILE="\<" fi fi # Part IIb Octave settings # ======================= # Skip this if you aren't using mode 2 if [ "$FSL_FIX_MATLAB_MODE" -eq 2 ]; then # Point this variable at your Octave command (or leave it blank to disable Octave mode) # Linux: if [ -z "${FSL_FIX_OCTAVE}" ]; then FSL_FIX_OCTAVE=$(which octave 2>/dev/null) #FSL_FIX_OCTAVE="/usr/bin/octave" #Linux #FSL_FIX_OCTAVE="/opt/local/bin/octave" # Mac OS X installed via MacPorts if [ -z "${FSL_FIX_OCTAVE}" ]; then echo "Please set FSL_FIX_OCTAVE variable in the settings.sh file to point at your MATLAB program" >2 fi fi # Set this to the Octave start-up options. Typically you will need to # enable 'MATLAB' mode (--traditional) and disable display output if [ -z "${FSL_FIX_OCOPTS}" ]; then FSL_FIX_OCOPTS="--traditional -q --no-window-system" fi # Set this to the Octave 'evaluate string' option if [ -z "${FSL_FIX_OCEVAL}" ]; then FSL_FIX_OCEVAL="--eval" fi # Set this to the pass in file option if [ -z "${FSL_FIX_OCFILE}" ]; then FSL_FIX_OCFILE="" fi fi # Part III R Settings # =================== if [ -z "${FSL_FIX_R_CMD}" ]; then FSL_FIX_R_CMD="/usr/bin/R" if [ ! -x "${FSL_FIX_R_CMD}" ]; then # Set this to the location of the R binary, e.g. # Linux: /usr/bin/R # macOS: $FSLDIR/fslpython/envs/fslpython/bin/R FSL_FIX_R_CMD=$(which R 2>/dev/null) fi if [ -z "${FSL_FIX_R_CMD}" ]; then echo "R not found - please set FSL_FIX_R_CMD to point to it in the settings.sh file" >2 fi fi # Part IV General settings # ========================= # Set this to CIFTI Matlab Reader/Writer for use within HCP pipelines # i.e., location of the ciftiopen.m, ciftisave.m, and ciftisavereset.m functions # https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB? # Note that the GIFTI library will need to be in your matlab/octave path as well (see previous link) # This variable is only relevant if using FSL_FIX_MATLAB_MODE of 1 or 2. # [If using the compiled version of FIX, the CIFTI I/O functionality is already part of the compiled executables]. if [ -z "${FSL_FIX_CIFTIRW}" ]; then FSL_FIX_CIFTIRW='~/projects/Pipelines/global/matlab/@gifti/gifti-1.6'; fi if [ -z "${FSL_FIX_WBC}" ]; then FSL_FIX_WBC="$(which wb_command 2>/dev/null)" if [ -z "${FSL_FIX_WBC}" ]; then # Set this to the location of the HCP Workbench folder for your platform #WBENCH="/opt/fmrib/workbench/" if [ "${FSL_FIX_OS}" = "Darwin" ]; then FSL_FIX_WBC="${WBENCH}/bin_macosx64/wb_command" elif [ "${FSL_FIX_OS}" = "Linux" ]; then FSL_FIX_WBC="/usr/bin/wb_command" fi fi fi export FSL_FIX_CIFTIRW FSL_FIX_WBC # Set this to the location of the FSL MATLAB scripts if [ -z "${FSLDIR}" ]; then echo "FSLDIR is not set - FIX will not be able to run" fi FSL_FIX_FSLMATLAB="${FSLDIR}/etc/matlab" ############################################################# # reset errexit if [ "$cur_errexit" = "on" ]; then set -o errexit fi