Need to know the variables in the laugher script.
Peace,
Matt.
On 8/22/17, 1:35 PM, "Kim, Sang-Young" <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>
>>wrote:
>>
>> How did you call the pipeline?
>>
>> Peace,
>>
>> Matt.
>>
>> On 8/22/17, 10:57 AM, "hcp-users-boun...@humanconnectome.org on behalf
>>of
>> Kim, Sang-Young" <hcp-users-boun...@humanconnectome.org on behalf of
>> 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
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>>
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