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Docker Run gave nothing, not results, no errors too. #178
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Hi Lei,
This is often because the dataset cannot be found. Can you go into the
container as you did in your second snippet, and instead run `ls
/home/data` to make sure the data has been mounted?
Thanks,
Greg
--
Greg Kiar <gkiar07@gmail.com>
…On Thu, Nov 1, 2018 at 3:01 PM Lei Ai ***@***.***> wrote:
Hi,
This is Lei Ai from the Child Mind Institute. I pulled the docker image
and tried to run some dataset (BIDS format), but a few seconds after
running the following commands, it 'finished/stopped.', no errors and
output.
Command run:
Outsied the docker:
docker run -ti --name ndmg_test --rm -v $datain:/home/data bids/ndmg
/home/data/ /home/data/outputs participant --participant_label 10001
Goign into the docker and run Inside:
docker run -ti -v $datain:/home/data --entrypoint /bin/bash bids/ndmg
ndmg_bids /home/data /home/data/output participant --participant_label
10001
$datain is the bids format dataset. I have tried with and without the
"--participant_label", there had the same problem.
Thank you very much.
Best,
Lei
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I did it the first time when it was not working, the actual data was there. Though I only have anatomical and functional data. I also run the ndmg_demo_dwi, it worked. This demo created one subject data. Then I run this sample subject the same way I run my own data, and it worked! The sample data is just in bids format and I don’t see any difference with my own dataset. I noticed it I did notice that when I first tried, my dataset was not in bids format, and the pipeline complained and gave errors. But once I input BIDS dataset, it has that problem. Thanks. |
Hi @hahaai which docker container are you using? It looks like you are using Can you show the result of the following command:
as well as the version of the docker container you are using, to confirm my suspicion? |
@ebridge2 Thanks. bids/ndmg latest 38f48d5df135 9 months ago 2.04GB Thank you very much. |
Hi @hahaai, the problem is your dataset has |
Briefly "sess-#" is not BIDs. Try again with "ses-#". See
https://bids.neuroimaging.io/bids_spec.pdf page 47for details onBIDs spec
will type more thorough response when at desktop
…On Thu, Nov 1, 2018 at 9:11 PM Lei Ai ***@***.***> wrote:
@ebridge2 <https://github.com/ebridge2> Thanks.
Here is one of my sample dataset tree.
[image: screen shot 2018-11-01 at 9 06 49 pm]
<https://user-images.githubusercontent.com/7807411/47888304-1bb28380-de1a-11e8-9179-4ae570713d3e.png>
Information about hte docker container. It seems it is a old one. What
about the neurodata/ndmg?
REPOSITORY TAG IMAGE ID CREATED SIZE
bids/ndmg latest 38f48d5df135 9 months ago 2.04GB
Thank you very much.
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Eric Bridgeford
ericwb.me
|
@hahaai try this: Pull docker container:
Download/unpack bids data (note you must have aws cli installed):
Run fmri pipeline:
Run dmri pipeline:
where all items in <> are for you to replace. |
Hey @hahaai have you had a chance to take a stab at the above example, and see if the |
Thanks. That worked after changed one thing: docker run -ti -v </path/local>/BIDs_test:/inputs -v </path/local/out>:/outputs neurodata/m3r-release:0.1.1 /inputs /outputs participant -- modality func --stc interleaved --nproc Another question, is that possible to do global regression? |
Hi @hahaai; yes, I made some changes last week to make it more compliant with BIDs containers since I last posted that comment, one of which was the flag change you found, so I apologize for not updating the issue accordingly! Re: GSR When we designed ndmg, our goal was to create a preprocessing pipeline suitable for most datasets as reliably as possible, so that aggregated inference could be performed without the afforementioned issues. When we made the decision to skip over gsr, that decision was made because when analyzing task fMRI, gsr basically destroyed a large component of the signal present using many common task fMRI analysis techniques. Recently, we are looking at adding a limited suite of command line options (such as whether or not to perform gsr; particularly, we found gsr to perform awesomely for resting state data, so this is why we are considering adding it back), but no decisions have been made yet. Your thoughts of why: to include gsr vs to not include gsr are much appreciated. Stay tuned! |
Hi,
This is Lei Ai from the Child Mind Institute. I pulled the docker image and tried to run some dataset (BIDS format), but a few seconds after running the following commands, it 'finished/stopped.', no errors and output.
Command run:
Outsied the docker:
docker run -ti --name ndmg_test --rm -v $datain:/home/data bids/ndmg /home/data/ /home/data/outputs participant --participant_label 10001
Goign into the docker and run Inside:
docker run -ti -v $datain:/home/data --entrypoint /bin/bash bids/ndmg
ndmg_bids /home/data /home/data/output participant --participant_label 10001
$datain is the bids format dataset. I have tried with and without the "--participant_label", there had the same problem.
Thank you very much.
Best,
Lei
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