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SetUpHCPPipeline_MSMRemoveGroupDrift.sh
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#!/bin/bash
script_name="SetUpHCPPipeline_MSMRemoveGroupDrift.sh"
echo "${script_name}: This script must be SOURCED to correctly setup the environment prior to running"
echo "${script_name}: any of the other HCP scripts contained here."
if [ "${COMPUTE}" = "" ]; then
echo "${script_name}: COMPUTE value unset. Setting to the default of CHPC"
export COMPUTE="CHPC"
fi
if [ "$COMPUTE" = "CHPC" ] ; then
echo ""
echo "${script_name}: Setting up for processing on ${COMPUTE}"
if [ "${CLUSTER}" = "1.0" ] ; then
echo ""
echo "${script_name}: Setting up FSL"
export FSLDIR=/export/fsl-5.0.6-20150401
source ${FSLDIR}/etc/fslconf/fsl.sh
echo "${script_name}: Set up to use FSL at ${FSLDIR}"
echo ""
echo "${script_name}: Setting up FreeSurfer"
export FSL_DIR="${FSLDIR}"
export FREESURFER_HOME=/export/freesurfer-5.3-HCP
source ${FREESURFER_HOME}/SetUpFreeSurfer.sh
echo "${script_name}: Set up to use FreeSurfer at ${FREESURFER_HOME}"
echo ""
echo "${script_name}: Setting up Python"
export EPD_PYTHON_HOME=/export/epc-7.3.2
export PATH=${EPD_PYTHON_HOME}/bin:${PATH}
echo "${script_name}: Set up to use EPD Python at ${EPD_PYTHON_HOME}"
echo ""
echo "${script_name}: Setting up Workbench (a.k.a. CARET7)"
export CARET7DIR=/export/HCP/workbench-v1.2.0-pre1/bin_rh_linux64
echo "${script_name}: Set up to use Workbench at ${CARET7DIR}"
echo ""
echo "${script_name}: Setting up HCP Pipelines"
export HCPPIPEDIR=/home/HCPpipeline/pipeline_tools/Pipelines_MSMRemoveGroupDrift
export HCPPIPEDIR_Config=${HCPPIPEDIR}/global/config
export HCPPIPEDIR_Global=${HCPPIPEDIR}/global/scripts
export HCPPIPEDIR_Templates=${HCPPIPEDIR}/global/templates
export HCPPIPEDIR_PreFS=${HCPPIPEDIR}/PreFreeSurfer/scripts
export HCPPIPEDIR_FS=${HCPPIPEDIR}/FreeSurfer/scripts
export HCPPIPEDIR_PostFS=${HCPPIPEDIR}/PostFreeSurfer/scripts
export HCPPIPEDIR_fMRISurf=${HCPPIPEDIR}/fMRISurface/scripts
export HCPPIPEDIR_fMRIVol=${HCPPIPEDIR}/fMRIVolume/scripts
export HCPPIPEDIR_dMRI=${HCPPIPEDIR}/DiffusionPreprocessing/scripts
export HCPPIPEDIR_tfMRIAnalysis=${HCPPIPEDIR}/TaskfMRIAnalysis/scripts
export HCPPIPEDIR_FIX=${HCPPIPEDIR}/catalog/FIX_HCP/resources/scripts
echo "${script_name}: Set up to use HCP Pipelines at ${HCPPIPEDIR}"
export MSMBin=/home/HCPpipeline/pipeline_tools/MSM-2015.01.14-RHEL5
echo "${script_name}: Set up to use MSM binary at ${MSMBin}"
export OCTAVE_HOME=/export/octave-3.6.3
echo "${script_name}: Set up to use Octave at ${OCTAVE_HOME}"
elif [ "${CLUSTER}" = "2.0" ] ; then
echo ""
echo "${script_name}: Setting up for CHPC cluster ${CLUSTER}"
echo ""
echo "${script_name}: Setting up FSL"
export FSLDIR=/export/HCP/fsl-5.0.6-20150401
source ${FSLDIR}/etc/fslconf/fsl.sh
echo "${script_name}: Set up to use FSL at ${FSLDIR}"
echo ""
echo "${script_name}: Setting up FreeSurfer"
export FSL_DIR="${FSLDIR}"
export FREESURFER_HOME=/act/freesurfer-5.3-HCP
source ${FREESURFER_HOME}/SetUpFreeSurfer.sh
echo "${script_name}: Set up to use FreeSurfer at ${FREESURFER_HOME}"
echo ""
echo "${script_name}: Setting up Python"
export EPD_PYTHON_HOME=${HOME}/export/epc-7.3.2
export PATH=${EPD_PYTHON_HOME}/bin:${PATH}
echo "${script_name}: Set up to use EPD Python at ${EPD_PYTHON_HOME}"
echo ""
echo "${script_name}: Setting up Workbench (a.k.a. CARET7)"
export CARET7DIR=/export/HCP/workbench-v1.2.0-pre1/bin_rh_linux64
echo "${script_name}: Set up to use Workbench at ${CARET7DIR}"
echo ""
echo "${script_name}: Setting up HCP Pipelines"
export HCPPIPEDIR=${HOME}/pipeline_tools/Pipelines_MSMRemoveGroupDrift
export HCPPIPEDIR_Config=${HCPPIPEDIR}/global/config
export HCPPIPEDIR_Global=${HCPPIPEDIR}/global/scripts
export HCPPIPEDIR_Templates=${HCPPIPEDIR}/global/templates
export HCPPIPEDIR_PreFS=${HCPPIPEDIR}/PreFreeSurfer/scripts
export HCPPIPEDIR_FS=${HCPPIPEDIR}/FreeSurfer/scripts
export HCPPIPEDIR_PostFS=${HCPPIPEDIR}/PostFreeSurfer/scripts
export HCPPIPEDIR_fMRISurf=${HCPPIPEDIR}/fMRISurface/scripts
export HCPPIPEDIR_fMRIVol=${HCPPIPEDIR}/fMRIVolume/scripts
export HCPPIPEDIR_dMRI=${HCPPIPEDIR}/DiffusionPreprocessing/scripts
export HCPPIPEDIR_tfMRIAnalysis=${HCPPIPEDIR}/TaskfMRIAnalysis/scripts
export HCPPIPEDIR_FIX=${HCPPIPEDIR}/catalog/FIX_HCP/resources/scripts
echo "${script_name}: Set up to use HCP Pipelines at ${HCPPIPEDIR}"
export MSMBin=${HOME}/pipeline_tools/MSM-2015.01.14
echo "${script_name}: Set up to use MSM binary at ${MSMBin}"
export OCTAVE_HOME=/export/octave-3.6.3
echo "${script_name}: Set up to use Octave at ${OCTAVE_HOME}"
else # unhandled value for ${CLUSTER}
echo "${script_name}: Processing set up for cluster ${CLUSTER} is currently not supported."
echo "${script_name}: EXITING WITH NON-ZERO EXIT STATUS (UNSUCCESSFUL EXECUTION)"
exit 1
fi
else # unhandled value for ${COMPUTE}
echo "${script_name}: Processing setup for ${COMPUTE} is currently not supported."
echo "${script_name}: EXITING WITH NON-ZERO EXIT STATUS (UNSUCCESSFUL EXECUTION)"
exit 1
fi