environment

# to source the MINC toolkit
source %MINC_TOOLKIT_DIR%/minc-toolkit-config.sh
umask 0002

# export PATH, PERL5LIB, TMPDIR and LORIS_CONFIG variables
export PATH=/data/%PROJECT%/bin/mri:/data/%PROJECT%/bin/mri/uploadNeuroDB:/data/%PROJECT%/bin/mri/uploadNeuroDB/bin:/data/%PROJECT%/bin/mri/dicom-archive:/data/%PROJECT%/bin/mri/python:/data/%PROJECT%/bin/mri/tools:/data/%PROJECT%/bin/mri/python/react-series-data-viewer:%MINC_TOOLKIT_DIR%/bin:$PATH
export PERL5LIB=/data/%PROJECT%/bin/mri/uploadNeuroDB:/data/%PROJECT%/bin/mri/dicom-archive:$PERL5LIB
export TMPDIR=/tmp
export LORIS_CONFIG=/data/%PROJECT%/bin/mri/dicom-archive

# for the Python scripts
export LORIS_MRI=/data/%PROJECT%/bin/mri
export PYTHONPATH=$PYTHONPATH:/data/%PROJECT%/bin/mri/python:/data/%PROJECT%/bin/mri/python/react-series-data-viewer
source /data/%PROJECT%/bin/mri/python_virtualenvs/loris-mri-python/bin/activate

# for the defacing scripts
export BEASTLIB=%MINC_TOOLKIT_DIR%/../share/beast-library-1.1
export MNI_MODELS=%MINC_TOOLKIT_DIR%/../share/icbm152_model_09c