# vbmeg resource file for bash shell.
export LD_LIBRARY_PATH=

# for FreeSurfer
FREESURFER_HOME=/home/cbi-data20/common/software/external/freesurfer/freesurferv6.0.0
source ${FREESURFER_HOME}/SetUpFreeSurfer.sh

# for FSL
FSLDIR=/home/cbi-data20/common/software/external/fsl/fsl6.0.6.4
. ${FSLDIR}/etc/fslconf/fsl.sh
PATH=${FSLDIR}/bin:${PATH}
if [ -e ${FSLDIR}/fslpython/lib/libstdc++.so.6 ]; then
    # for before FSL 6.0.5.2 and older
    LD_PRELOAD=${FSLDIR}/fslpython/lib/libstdc++.so.6
elif [ -e ${FSLDIR}/lib/libstdc++.so.6 ]; then
    # for FSL 6.0.6 or later
    LD_PRELOAD=${FSLDIR}/lib/libstdc++.so.6
fi
export FSLDIR PATH LD_PRELOAD

# for MRtrix
MRTRIXDIR=/home/cbi-data20/common/software/external/mrtrix/mrtrix3-3.0.3
PATH=${MRTRIXDIR}/bin:${PATH}
export MRTRIXDIR PATH

# jq
JQPATH=/home/cbi-data20/common/software/external/jq/1.6
PATH=${JQPATH}:${PATH}
export PATH

# ANTs
export ANTSPATH=/home/cbi-data20/common/software/external/ANTS/v2.4.2/bin
PATH=$PATH:$ANTSPATH
export PATH

# To avoid "invalid charset name" error
unset LESSCHARSET

#
# --- Advanced
#

# To avoid using libstdc++.so.6 in MATLAB
LIBSTDC=$(find /usr/lib/*/libstdc++.so.6 2> /dev/null)
if [ $? = 0 ]; then
    export LD_PRELOAD=${LD_PRELOAD}:$LIBSTDC
fi
LIBSTDC=$(find /usr/lib64/libstdc++.so.6 2> /dev/null)
if [ $? = 0 ]; then
    export LD_PRELOAD=${LD_PRELOAD}:$LIBSTDC
fi
LIBSTDC=$(find /usr/lib/libstdc++.so.6 2> /dev/null)
if [ $? = 0 ]; then
    export LD_PRELOAD=${LD_PRELOAD}:$LIBSTDC
fi

