You need to update workbench to the latest release, that option is a recent
addition to the command that is failing.
Tim
On Tue, Oct 9, 2018 at 6:08 PM, ARMAN PRAFUL KULKARNI <apkulkar...@wisc.edu>
wrote:
> 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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> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
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