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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