qsiprep suddenly stops without an error message during preprocessing

[overjoyroy]

I am trying to run qsiprep and running into issues. I've attached a screenshot of the error I'm getting. I'm not sure why its occurring. It says "Sentry is attempting to send 2 pending error messages" but I'm not sure what that means or how to receive the error messages. The error always occurs after "Finished "ds_interactive_report" " and occurs whether I use a T1w or --dwi-only flag turned on.

I have inspected the outputted html file and it says that there are no errors to report.

The command that I use is the following:

docker run -ti --rm \
    -v ~/Desktop/test/myProj:/data \
    -v ~/Desktop/test/out:/out \
    -v ~/Desktop/test/license.txt:/opt/freesurfer/license.txt \
    pennbbl/qsiprep:latest \
    /data /out participant \
    --fs-license-file /opt/freesurfer/license.txt \
    --output-resolution 1.2 \
        --verbose

I have also included an example of the filesystem tree I'm using. It passes the BIDS checker, but I'm wondering if there is something the checker is missing that is causing issues.

[vnckppl]

Experiencing the exact same thing here. I am getting to the exact same point in the pipeline (same output files). The only difference is that I do have AP-PA images in an fmap folder.

[mattcieslak]

It looks like qsiprep finished successfully but your container is still running for some reason. Does the html report indicate anything went wrong?

[vnckppl]

Hi Matt, thanks for your reply.

• The html report indicates 'No errors to report!' under the Error section.
• docker ps does not show any active containers
• I re-reran the process with another subject from another study (different T1 and DWI seqeuences), but ran into the same issue.

I am running qsiprep version 0.17.0 via Docker, which I pulled yesterday. I will go ahead and run this on another machine. If you have a test data set that you know works with qsiprep, I can run the pipeline on that to identify what is causing the issue (my data, the installation of qsiprep on my machine, or a combination).

[mattcieslak]

here's a very small dataset we use for CI tests: https://github.com/PennLINC/qsiprep/blob/master/.circleci/get_data.sh#L328

[vnckppl]

I dowloaded the DSCSDSI_nofmap dataset and ran it on the same machine. It resulted in the same problem. I have explicitly saved the tmp folder to a path. A list of files in this folder is attached here: https://github.com/PennLINC/qsiprep/files/11521119/workdir.txt

Interestingly, the same code ran om another machine without issues. Differences and similatiries between the machines can be seen in this table:

	Machine 1	Machine 2
qsiprep finishes normally with all output?	no	yes
OS	Ubuntu 22.04	Debian 4.9.320-2
Docker	24.0.0, build 98fdcd7	17.09.0-ce, build afdb6d4
qsiprep Docker image ID	7ea5432a124e	7ea5432a124e
qsirprep version	0.17.0	0.17.0

Any suggestions on how to further troubleshoot qsiprep on Machine 1?

[mattcieslak]

I'm running locally on macOS with Docker version 23.0.5 and I'm not sure which version the CI tests use. If the hanging is still happening with that tiny dataset it's almost certainly not a memory issue. Is there anything in the logs directory in the outputs?

Also just to clarify - The "sending 2 error messages to sentry" shows up randomly, I'm not sure why yet. Unless there is a traceback or a crash log in the outputs then the actual workflow ran without a problem.

[vnckppl]

Thanks for the input. I was just updating Machine 1 yesterday evenenig and noticed there was a new incremental version of Docker available through my package manager (Docker version 24.0.1, build 6802122). After installing that, qsiprep finished with creating all the reports. I only tested it on one subject so far, but it seems promissing. Also, indeed the error/warning:

Sentry is attempting to send 2 pending error messages
Waiting up to 2 seconds
Press Ctrl-C to quit

still shows at the end of the log, but I understand that is not a problem.