Re: [HCP-Users] HCP Pipelines BIDS App

[Chris Gorgolewski]

On Thu, Jun 22, 2017 at 4:04 PM,  wrote:

> Hi Chris,
>
> Thank you for your response! This worked very well and I hope it will help
> others in the future.
> I am now trying to run the entire HCP pipeline on one subject, labeled
> "Asample", using the following command:
>
> ./bids_hcppipelines_v3.17.0-13-2016-11-02-c9c1c3cc2228.img
> /tmp/BIDS_HCP_test /tmp/BIDS_HCP_test/HCP_PreProc_output participant
> --participant_label Asample --license_key CX2frM4fbVCk
>
>
> I am getting the following error:
>
> Final FOV is:
> 0.00 176.00 0.00 256.00 89.00 150.00
>
> Image Exception : #22 :: ERROR: Could not open image
> /opt/HCP-Pipelines/global/templates/MNI152_T1_1.0mm
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /opt/HCP-Pipelines/PreFreeSurfer/scripts/ACPCAlignment.sh: line 84:  4731
> Aborted ${FSLDIR}/bin/flirt -interp spline -in
> "$WD"/robustroi.nii.gz -ref "$Reference" -omat "$WD"/roi2std.mat -out
> "$WD"/acpc_final.nii.gz -searchrx -30 30 -searchry -30 30 -searchrz -30 30
>
> Traceback (most recent call last):
>   File "/run.py", line 340, in 
> stage_func()
>   File "/run.py", line 69, in run_pre_freesurfer
> run(cmd, cwd=args["path"], env={"OMP_NUM_THREADS":
> str(args["n_cpus"])})
>   File "/run.py", line 28, in run
> raise Exception("Non zero return code: %d"%process.returncode)
> Exception: Non zero return code: 134
>
> It seems like /opt/HCP-Pipelines/global/templates/ is not in my HPC but
> rather in the container, is this correct?
>
This is a bug - I'm working on a fix
. Will get back to you.

Best,
Chris


> Could you please advise on ways to debug or things to try?
> Should I be using Joke's Singularity file at all? I see the HCPPIPEDIR in
> question on there.
>
> Any advice on how to proceed/troubleshoot would be greatly appreciated!
>
> Thanks,
> Paola Odriozola
>
>
>
>
>
> On Thursday, June 15, 2017 at 4:07:53 PM UTC-4, Chris Gorgolewski wrote:
>>
>>
>>
>> On Thu, Jun 15, 2017 at 1:00 PM,  wrote:
>>
>>> Dear Chris,
>>>
>>> Thank you for all your contributions to reproducible science! I've read
>>> your documentation and watched your neurohackweek video which have been
>>> really helpful, but I am still unclear on the specific command used to run
>>> the HCPpipeline BIDSapp using Singularity on an HPC. I see instructions for
>>> Docker commands here
>>> , but
>>> not Singularity,
>>>
>> There is more information here: http://bids-apps.neuroimaging.
>> io/tutorial/ and in the paper http://journals.plos.org
>> /ploscompbiol/article?id=10.1371/journal.pcbi.1005209
>>
>>
>>> I ran the following commands on my local computer to convert the image
>>> from docker to singularity:
>>>
>>> $ docker run --privileged -ti --rm  -v 
>>> /var/run/docker.sock:/var/run/docker.sock
>>> -v /Users/estee/Desktop/singularity_images:/output
>>> filo/docker2singularity bids/example:0.0.4
>>>
>>> Then I transferred this image to my HPC system (now named:
>>> bids_example_0.0.4-2016-08-28-fba9b3e0a751.img)  and installed
>>> Singularity. Is this the correct image file I should be using?
>>>
>> This command will create an image for the example app. To create one for
>> the  HCP Pipelines you need to replace "bids/example:0.0.4" with
>> "bids/hcppipelines:v3.17.0-13"
>>
>> What is the specific command I should be running to preprocess one
>>> subject using Singularity? Should I be running the run.py script within
>>> singularity? And how do I specify the subjectID or directory?
>>>
>> ./name_of_the_image.img  
>> participant --participant_label 
>>
>> You need to replace   
>> with values corresponding to your dataset.
>>
>> Please mind that HCP pipelines only work on datasets that include T2
>> weighted images and fieldmaps!
>>
>> Best,
>> Chris
>>
>>
>>
>>>
>>>
>>> Thanks,
>>> Paola
>>>
>>>
>>> On Sunday, September 11, 2016 at 1:03:32 AM UTC-4, Chris Gorgolewski
>>> wrote:

 Dear HCP community,

 Many researchers want to run HCP Pipelines on their own datasets, but
 run into problems with software dependencies and different organization of
 data and metadata. To help with this issue I have created an HCP Pipelines
 BIDS App. Like all other BIDS Apps 
 the HCP Pipelines one has the following features:

- It's portable (meaning comes with all of the dependencies with
the correct versions - no need to install FSL or Freesurfer).
- Runs on Windows, Mac OS X and Linux (as well as HPCs or clusters
via Singularity ).
- No need to specify any metadata - all you need as an input is a BIDS
dataset .
- The only software required (across all three platforms) is Docker

Re: [HCP-Users] Structural Protocol

[Harms, Michael]

Hi,
Check out the various “Connectomes Related to Disease” projects on the 
re-designed humanconnectome.org website.  A couple of them involve vision loss, 
and several involve individuals over the age of 60.  And of course the 
HCP-Aging project will include individuals over 60 as well.

Data from all these projects will be distributed eventually via the Connectome 
Coordination Facility at WU.

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
St. Louis, MO  63110 Email: mha...@wustl.edu

From: Rachel Woodall 
>
Date: Thursday, June 22, 2017 at 4:06 AM
To: Michael Harms >
Cc: "hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] Structural Protocol

Thanks for this Michael.
I'm acquiring structural scans on elderly patients with vision loss and 
age-matched sighted controls (age range 60-80+).  Are you aware of any other 
groups who are acquiring similar data sets of visually impaired and sighted 
controls of this age?  It might be useful to talk about sharing data as 
recruiting age-matched sighted controls is actually more difficult than 
recruiting patients.

Best wishes,
Rachel

On 21 June 2017 at 14:33, Harms, Michael 
> wrote:

Hi,
You can find an importable protocol here:
http://protocols.humanconnectome.org/CCF/

The protocols that we are using for the HCP-Aging/Development projects are 
highly similar, but include a few additions (e.g., switch to 
navigator-corrected anatomicals; addition of PCASL scan).  Those will be posted 
once we can organize the documentation (sometime after OHBM).

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
St. Louis, MO  63110Email: mha...@wustl.edu

From: 
>
 on behalf of Rachel Woodall 
>
Date: Wednesday, June 21, 2017 at 3:42 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Structural Protocol

Hello,

Is the Pheonix ZIP file available for the structural protocol on a 3T Siemens 
Prisma?

Many thanks,
Rachel

--
Rachel Woodall

PhD Student
University of York
Department of Psychology
YO10 5DD

Email: rachel.wood...@york.ac.uk
Phone: 01904 567613


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--
Rachel Woodall

PhD Student
University of York
Department of Psychology
YO10 5DD

Email: rachel.wood...@york.ac.uk
Phone: 01904 567613



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

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Re: [HCP-Users] Structural Protocol

[Rachel Woodall]

Thanks for this Michael.
I'm acquiring structural scans on elderly patients with vision loss and
age-matched sighted controls (age range 60-80+).  Are you aware of any
other groups who are acquiring similar data sets of visually impaired and
sighted controls of this age?  It might be useful to talk about sharing
data as recruiting age-matched sighted controls is actually more difficult
than recruiting patients.

Best wishes,
Rachel

On 21 June 2017 at 14:33, Harms, Michael  wrote:

>
> Hi,
> You can find an importable protocol here:
> http://protocols.humanconnectome.org/CCF/
>
> The protocols that we are using for the HCP-Aging/Development projects are
> highly similar, but include a few additions (e.g., switch to
> navigator-corrected anatomicals; addition of PCASL scan).  Those will be
> posted once we can organize the documentation (sometime after OHBM).
>
> 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:  on behalf of Rachel Woodall
> 
> Date: Wednesday, June 21, 2017 at 3:42 AM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] Structural Protocol
>
> Hello,
>
> Is the Pheonix ZIP file available for the structural protocol on a 3T
> Siemens Prisma?
>
> Many thanks,
> Rachel
>
> --
> Rachel Woodall
>
> PhD Student
> University of York
> Department of Psychology
> YO10 5DD
>
> Email: rachel.wood...@york.ac.uk
> Phone: 01904 567613
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>



-- 
Rachel Woodall

PhD Student
University of York
Department of Psychology
YO10 5DD

Email: rachel.wood...@york.ac.uk
Phone: 01904 567613

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