Hi Tim,
I have the updated version of workbench now, and have tried running the pipeline again. PostFreeSurferPipelineBatch.sh has now been running for over 5 hours. To my knowledge, prior to this update, it only took around 45 minutes when successful. Is this normal for this version of the pipeline to take this long? Thanks again. Sincerely, Arman ________________________________ From: Timothy Coalson <tsc...@mst.edu> Sent: Tuesday, October 9, 2018 6:13:44 PM To: ARMAN PRAFUL KULKARNI Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh 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<mailto: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 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
