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

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