Hi you need to install CUDA 7.5 and have
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/lib64 export LD_LIBRARY_PATH in your ~/.bashrc, assuming that /usr/local/cuda is where you have installed CUDA, otherwise replace accordingly. Cheers Stam On 22 Aug 2017, at 20:01, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Actually that looks like a cuda library error and your pipeline setup looks fine. You might ask on the FSL list about that. Peace, Matt. From: "Kim, Sang-Young" <sak...@pitt.edu<mailto:sak...@pitt.edu>> Date: Tuesday, August 22, 2017 at 1:55 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] dMRI: Error while running "run_eddy.sh" I’m sorry for misunderstanding. Yes, the Pipelines is in the ${HOME}/projects/Pipelines. The other pipelines such as PreFreeSurferPipeline, FreeSurferPipeline, PostFreeSurferPipeline, fMRIVolumePipeline and fMRISurfacePipeline can be run successfully without any errors. The followings are the variables in the DiffusionPreprocessingBatch script. ************************************************************************************* StudyFolder="/Volumes/LaCieMac3TB/HIV_HCP_pipeline/Data" Subjlist="30067" EnvironmentScript="${HOME}/projects/Pipelines/Examples/Scripts/SetUpHCPPipeline.sh" SubjectID="$Subject" RawDataDir="$StudyFolder/$SubjectID/unprocessed/3T/Diffusion" PosData="${RawDataDir}/${SubjectID}_3T_DWI_dir113_AP.nii.gz" NegData="${RawDataDir}/${SubjectID}_3T_DWI_dir113_PA.nii.gz" EchoSpacing=0.77 PEdir=2 Gdcoeffs="${HCPPIPEDIR_Config}/coeff_AS82_Prisma.grad" ************************************************************************************* Thanks. Sang-Young On Aug 22, 2017, at 2:44 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: I mean the launcher script not the environment script. Although is that really where you have ${HCPIPEDIR}? Peace, Matt. From: "Kim, Sang-Young" <sak...@pitt.edu<mailto:sak...@pitt.edu>> Date: Tuesday, August 22, 2017 at 1:42 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] dMRI: Error while running "run_eddy.sh" The followings are the variables in SetUpHCPPipeline.sh. *************************************************** export FSL_DIR=${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=/Applications/freesurfer source ${FREESURFER_HOME}/SetUpFreeSurfer.sh > /dev/null 2>&1 # Set up specific environment variables for the HCP Pipeline export HCPPIPEDIR=${HOME}/projects/Pipelines export CARET7DIR=/Applications/workbench/bin_macosx64 export MSMCONFIGDIR=${HCPPIPEDIR}/MSMConfig export MATLAB_COMPILER_RUNTIME=/Applications/MATLAB/MATLAB_Runtime/v91 export FSL_FIXDIR=/usr/local/fix export MSMBin=${HCPPIPEDIR}/MSMBinaries 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 ************************************************************** Thanks. Sang-Young On Aug 22, 2017, at 2:38 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Need to know the variables in the laugher script. Peace, Matt. On 8/22/17, 1:35 PM, "Kim, Sang-Young" <sak...@pitt.edu<mailto:sak...@pitt.edu>> wrote: Dear Matt: Since I have added path for batch scripts, I just ran the pipeline in the terminal as follow: DiffusionPreprocessingBatch.sh I believe all environment variables are correctly set in "SetUpHCPPipeline.sh". Thanks. Sang-Young On Aug 22, 2017, at 2:28 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: How did you call the pipeline? Peace, Matt. On 8/22/17, 10:57 AM, "hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> on behalf of Kim, Sang-Young" <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> on behalf of sak...@pitt.edu<mailto:sak...@pitt.edu>> wrote: Dear HCP experts: We have diffusion MRI data acquired from Siemens Prisma 3 T scanner. The dMRI data were acquired with 113 diffusion direction and AP phase encoding. The b0 images were acquired with opposite phase encoding direction for topup. I would like to preprocess dMRI data using DiffusionPreprocessing pipeline provided from HCP. So I ran the DiffusionPreprocessingBatch.sh file with minor modification for scan setting and gradient nonlinearity correction. But error message came up while running "run_eddy.sh". Please see below: **************************************************************** dyld: Library not loaded: @rpath/libcudart.7.5.dylib Referenced from: /usr/local/fsl/bin/eddy_cuda Reason: image not found /Users/sang-young/projects/Pipelines/DiffusionPreprocessing/scripts/run_ ed dy.sh: line 380: 16731 Abort trap: 6 ${eddy_command} ****************************************************************** Does anybody have similar problem? Any insights would be greatly appreciated. Thanks in advance. Sang-Young Kim, Ph.D. Postdoctoral Research Fellow Department of Radiology, University of Pittsburgh _______________________________________________ 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<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ 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<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ 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
