Hi,
I have been running the HCP Pipeline (v 3.27.0) on one subject's unprocessed
data from the HCP-1200 dataset. Below is what I have in the SetUpHCPPipeline.sh
file. I have been able to run PreFreeSurferPipelineBatch.sh and
FreeSurferPipelineBatch.sh with no issues. However, when running
PostFreeSurferPipelineBatch.sh, I get the following error after around 10
minutes of the script running: "ERROR: Unexpected parameter:
-local-affine-method", and I am not sure how to proceed. I appreciate any
insight into this problem.
Sincerely,
Arman
-------
#!/bin/bash
echo "This script must be SOURCED to correctly setup the environment prior to
running any of the other HCP scripts contained here"
# Set up FSL (if not already done so in the running environment)
# Uncomment the following 2 lines (remove the leading #) and correct the FSLDIR
setting for your setup
#export FSLDIR=/usr/share/fsl/5.0
#. ${FSLDIR}/etc/fslconf/fsl.sh
# Let FreeSurfer know what version of FSL to use
# FreeSurfer uses FSL_DIR instead of FSLDIR to determine the FSL version
export FSL_DIR="${FSLDIR}"
# Set up FreeSurfer (if not already done so in the running environment)
# Uncomment the following 2 lines (remove the leading #) and correct the
FREESURFER_HOME setting for your setup
#export FREESURFER_HOME=/usr/local/bin/freesurfer
#source ${FREESURFER_HOME}/SetUpFreeSurfer.sh > /dev/null 2>&1
# Set up specific environment variables for the HCP Pipeline
export HCPPIPEDIR=${HOME}/xxxx/HCP/Pipelines
#export CARET7DIR=${HOME}/tools/workbench/bin_rh_linux64
export CARET7DIR=/usr/local/workbench/bin_linux64
export HCPPIPEDIR_Templates=${HCPPIPEDIR}/global/templates
export HCPPIPEDIR_Bin=${HCPPIPEDIR}/global/binaries
export HCPPIPEDIR_Config=${HCPPIPEDIR}/global/config
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=${HCPPIPEDIR}/fMRIVolume/scripts
export HCPPIPEDIR_tfMRI=${HCPPIPEDIR}/tfMRI/scripts
export HCPPIPEDIR_dMRI=${HCPPIPEDIR}/DiffusionPreprocessing/scripts
export HCPPIPEDIR_dMRITract=${HCPPIPEDIR}/DiffusionTractography/scripts
export HCPPIPEDIR_Global=${HCPPIPEDIR}/global/scripts
export HCPPIPEDIR_tfMRIAnalysis=${HCPPIPEDIR}/TaskfMRIAnalysis/scripts
export MSMBINDIR=${HCPPIPEDIR}/global/templates/MSMAll
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