Re: [HCP-Users] HCP Pipelines BIDS App
Hi,
I release a new version with a bugfix: v3.17.0-14. Please give it a try,
Best,
Chris
On Thu, Jun 22, 2017 at 1:43 PM, Chris Gorgolewski <
krzysztof.gorgolew...@gmail.com> wrote:
> 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
Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
thank you very much!I have the standard Freesurfer version! I m going to try to the HCP one now! Maria Luisa Mandelli, PhD Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ From: Dierker, Donna Sent: Monday, June 26, 2017 11:54:40 AM To: Mandelli, Maria Luisa Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found Many of the HCP experts are at OHBM, so replies might take longer. I know from my own experience with HCP output to look here for the Freesurfer subject directories: subject-id/T1w/subject-id/label/* subject-id/T1w/subject-id/mri/* subject-id/T1w/subject-id/surf/* … Also see page 21 here: http://humanconnectome.org/storage/app/media/documentation/s1200/HCP_S1200_Release_Appendix_III.pdf Hopefully there is no problem! :) But I must point out that there is a difference between the Freesurfer v5.3 distribution and Freesurfer 5.3-HCP. The latter uses both T1w & T2w images, which makes a big difference (e.g., for myelin maps). Not sure which you used, but it is an important difference. > On Jun 26, 2017, at 12:27 PM, Mandelli, Maria Luisa > wrote: > > Hi! > I m running the structural HCP pipeline and I m using Freesurfer v5.3 > It seems that the job finished without errors but I dont see the files in the > T1w folder of the subject. > For example the wmparc_1mm files > I m not sure where is the problem! > Thank you > > > Maria Luisa Mandelli, PhD > Assistant Professional Researcher > > University of California, San Francisco > 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 > > Language Neurobiology Lab > http://albalab.ucsf.edu/ > Memory and Aging Center > http://memory.ucsf.edu/ > UCSF Dyslexia Center > http://dyslexia.ucsf.edu/ > > ___ > 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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] harmonizing data
I have a question/request that I know is unusual but that I'm hoping you'll consider. I help to lead a small group of researchers at the Minnesota Center for Twin and Family Research at the University of Minnesota interested in understanding effects of substance use and abuse on brain development in adolescence and early adulthood. Alcohol consumption can be characterized in different ways and it isn't immediately apparent what is most relevant for effects on brain structure and function. We have therefore created an index of alcohol use that combines 4 different aspects of exposure: typical quantity consumed in the past year, frequency of past-year consumption, density of consumption (maximum number of drinks consumed in a single 24-hr period), and misuse (number of times drinking to the point of intoxication). We have "ordinalized" the distribution of responses to these 4 different questions by grouping together similar responses, and the index derived from these ordinalized versions of the original variables has good psychometric properties and appears to work well as a measure of alcohol exposure; we are obtaining several interesting associations in our sample of twins with MRI and EEG data, including apparent causal effects of exposure in twin-difference analyses. I personally am interested in using data from the HCP, and I'm part of a different group here at the U of MN doing so with approval from the IRB here. I'd like to create a similar index of alcohol use from the relevant SSAGA questions asked of HCP participants. However, responses to these questions have been categorized/ordinalized differently than we have done at the MCTFR. In particular, the HCP version has greater sensitivity at the low end of alcohol use, whereas the MCTFR version has greater sensitivity at higher levels of use. I'm interested in replicating findings in one data set in the other data set, or in combining results of the two analyses through meta-analysis. To do so, it would clearly be best to use as similar a method of categorizing responses in both as possible. Given that we have good evidence of the effectiveness of our approach, it would be ideal to use a similar method with the HCP data. However, that would require having the original, uncategorized variables in order to create categories similar to ours. I know that this is an unusual request, but is it possible to obtain a file with the 3 or 4 original variables I'm interested in? I'd obviously be happy to answer any questions or address any concerns you might have about this. Sincerely, Steve - Steve Malone Research Assistant Professor MN Center for Twin & Family Research Department of Psychology University of Minnesota 612/626-1436 (voice) 612/626-2079 (fax) ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found
Many of the HCP experts are at OHBM, so replies might take longer. I know from my own experience with HCP output to look here for the Freesurfer subject directories: subject-id/T1w/subject-id/label/* subject-id/T1w/subject-id/mri/* subject-id/T1w/subject-id/surf/* … Also see page 21 here: http://humanconnectome.org/storage/app/media/documentation/s1200/HCP_S1200_Release_Appendix_III.pdf Hopefully there is no problem! :) But I must point out that there is a difference between the Freesurfer v5.3 distribution and Freesurfer 5.3-HCP. The latter uses both T1w & T2w images, which makes a big difference (e.g., for myelin maps). Not sure which you used, but it is an important difference. > On Jun 26, 2017, at 12:27 PM, Mandelli, Maria Luisa > wrote: > > Hi! > I m running the structural HCP pipeline and I m using Freesurfer v5.3 > It seems that the job finished without errors but I dont see the files in the > T1w folder of the subject. > For example the wmparc_1mm files > I m not sure where is the problem! > Thank you > > > Maria Luisa Mandelli, PhD > Assistant Professional Researcher > > University of California, San Francisco > 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 > > Language Neurobiology Lab > http://albalab.ucsf.edu/ > Memory and Aging Center > http://memory.ucsf.edu/ > UCSF Dyslexia Center > http://dyslexia.ucsf.edu/ > > ___ > 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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] pipeline structural PostFreesurfer wmparc not found
Hi! I m running the structural HCP pipeline and I m using Freesurfer v5.3 It seems that the job finished without errors but I dont see the files in the T1w folder of the subject. For example the wmparc_1mm files I m not sure where is the problem! Thank you Maria Luisa Mandelli, PhD Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
