Thanks for the reply.
I would like to reduce the computing time for DiffusionPreprocessing;
feeding in both sets of dMRIs takes about 24.16 hours to run, while
parallel processing takes 10.72 hours.
I've been trying to retrieve the eddy_cuda version, but I can't find it in
the neurodebian packages. Where can I find pre-compiled binaries of
eddy_cuda?
The platform I am using in my Docker is Ubuntu 14.04 LTS.
Thank you again,
Yeun
On Mon, Jul 17, 2017 at 11:57 AM, Harms, Michael <mha...@wustl.edu> wrote:
>
> Hi,
> Is there a particular reason that you can’t provide all the dMRI scans at
> once, and let the pipeline handle the merging for you?
> If you process each dMRI run separately, then the individual runs will not
> be in optimal alignment. (You would be relying on the registration of each
> run to the T1, rather than registering the dMRI directly to each other as
> part of ‘eddy’).
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
> -----------------------------------------------------------
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173 <(314)%20747-6173>
> St. Louis, MO 63110 Email: mha...@wustl.edu
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of Yeun Kim <
> yeun...@gmail.com>
> Date: Monday, July 17, 2017 at 1:32 PM
> To: "Glasser, Matthew" <glass...@wustl.edu>
>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] diffusion data merge pipeline
>
> I am using the following function (and is looped through the pairs of
> unique sets of gradient tables (i.e. loops twice for dir99 and dir98):
> ${HCPPIPEDIR}/DiffusionPreprocessing/DiffPreprocPipeline.sh \
> --posData="{posData}" \
> --negData="{negData}" \
> --path="{path}" \
> --subject="{subject}" \
> --echospacing="{echospacing}" \
> --PEdir={PEdir} \
> --gdcoeffs="NONE" \
> --dwiname="{dwiname}" \
> --printcom=""'
>
> Where:
> $posData = diffusion data in the positive direction
> $negData = diffusion data in the negative direction
> $path = output directory path
> $echospacing = echospacing
> $PEdir = 2
> $dwiname = i.e. Diffusion_dir-98_run-01
>
>
> FYI: I'm using HCPPipelines v3.17.
>
> -------------------------------------------------------------
>
> Technical details:
>
> I run ${HCPPIPEDIR}/DiffusionPreprocessing/DiffPreprocPipeline.sh in a
> Docker container with the following python code. It is looped through the
> pairs of unique sets of gradient tables (i.e. loops twice for dir99 and
> dir98) and set to process in parallel:
>
> dwi_stage_dict = OrderedDict([("DiffusionPreprocessing",
> partial(run_diffusion_processsing,
>
> *posData*=pos,
>
> *negData*=neg,
>
> *path*=args.output_dir,
>
> *subject*="sub-%s" % subject_label,
>
> *echospacing*=echospacing,
>
> *PEdir*=PEdir,
>
> *gdcoeffs*="NONE",
>
> *dwiname*=dwiname,
>
> *n_cpus*=args.n_cpus))])
> for stage, stage_func in
> dwi_stage_dict.iteritems():
> if stage in args.stages:
> Process(target=stage_func).start()
>
> On Mon, Jul 17, 2017 at 11:15 AM, Glasser, Matthew <glass...@wustl.edu>
> wrote:
>
>> The pipeline is capable of doing the merge for you if you want. Can you
>> post how you called the diffusion pipeline?
>>
>> Peace,
>>
>> Matt.
>>
>> From: Yeun Kim <yeun...@gmail.com>
>> Date: Monday, July 17, 2017 at 1:12 PM
>> To: Matt Glasser <glass...@wustl.edu>
>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Subject: Re: [HCP-Users] diffusion data merge pipeline
>>
>> When I run DiffusionPreprocessing, I make the --dwiname=DWIName specific
>> to the diffusion scan (i.e. DWIName= Diffusion_dir-98_run-01) to prevent
>> files from being overwritten.
>> I end up with:
>> ${StudyFolder}/${Subject}/T1w/Diffusion_dir-98_run-01/data.nii.gz
>> ${StudyFolder}/${Subject}/T1w/Diffusion_dir-99_run-01/data.nii.gz
>>
>> I would like to combine the two data.nii.gz files.
>>
>> On Mon, Jul 17, 2017 at 10:58 AM, Glasser, Matthew <glass...@wustl.edu>
>> wrote:
>>
>>> Look for the ${StudyFolder}/${Subject}/T1w/Diffusion/data.nii.gz file.
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Yeun Kim <
>>> yeun...@gmail.com>
>>> Date: Monday, July 17, 2017 at 12:56 PM
>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>> Subject: [HCP-Users] diffusion data merge pipeline
>>>
>>> Hi,
>>>
>>> We have the diffusion scans:
>>> dMRI_dir98_AP, dMRI_dir98_PA
>>> dMRI_dir99_AP, dMRI_dir99_PA
>>>
>>> in which there is a pair of phase encoding directions (AP,PA) and two
>>> sets of different diffusion weighting directions (dir98 and dir99).
>>>
>>> After running the DiffusionPreprocessing module of the HCP minimal
>>> preprocessing pipeline, I would like to merge the processed dMRI_dir98 and
>>> dMRI_dir99 data. Do you have any suggestions on how to perform this step?
>>> Also, are there any workflows developed by HCP for
>>> post-DiffusionPreprocessing?
>>>
>>> Thank you,
>>> Yeun
>>>
>>> _______________________________________________
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>
>>
>>
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