fix_settings.sh

# Settings file for FIX
# Modify these settings based on your system setup
FIXVERSION=1.06
#   (actually this version is 1.068 - see wiki page for details)

# 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

# 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="/opt/matlabmcr-2017b"
		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 [ "$FSL_FIX_MATLAB_MODE" -eq 1 ]; then
	# Look for installed MATLAB
	MATLAB_BIN=/opt/matlabmcr-2017b
	if [ -z "${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 "${FSL_FIX_CIFTIRW}" ]; then
	FSL_FIX_CIFTIRW='/opt/fmrib/workbench_ciftireader/CIFTIMatlabReaderWriter';
fi
if [ -z "${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 [ "${FSL_FIX_OS}" = "Linux" ]; then
			FSL_FIX_WBC="${WBENCH}/bin_linux64/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