fMRIPrep in neurodesk BrokenProcessPool error

Software Support
,
1

Summary of what happened:

Dear all,

I am seeing the following error while running fmriprep in Neurodesk (on a Windows machine):

The answers I found online suggest that this reflects insufficient memory. However, this does not seem to be the case based on what I see on the bottom right corner of the file explorer (attached).

I am unsure how to proceed. Any advice would be highly appreciated.

Thank you,
Lavinia

Command used (and if a helper script was used, a link to the helper script or the command generated):

fmriprep \
/home/jovyan/neurodesktop-storage/RSNE/bids \
/home/jovyan/neurodesktop-storage/RSNE \
-w work/ \
participant \
--participant-label sub-006 \
--level full \
--cifti-output 170k \
--fs-license-file /home/jovyan/freesurfer-subjects-dir/.license.txt

Version:

23.2.1

Environment (Docker, Singularity / Apptainer, custom installation):

Docker via Neurodesk on Windows

Data formatted according to a validatable standard? Please provide the output of the validator:

image
image1380×732 99.2 KB

Relevant log outputs (up to 20 lines):

concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.

Screenshots / relevant information:

ram usage
ram usage746×104 18.7 KB

image
image1471×911 123 KB

2

Hi @lavinia.carmen.u and welcome to neurostars!

There is not a lot of information here for us to help debug. We have a Software Support template that prompts you for important information. You can see I have edited your post to add the template in, and you can edit your post to add the missing information.

Also, in your image you highlighted memory as in storage, while the error is indicating a lack of job-specific memory or RAM.

Best,
Steven

3

ram usage
ram usage746×104 18.7 KB

Hi, Steven,

Thank you for your quick reply!
Indeed, I only realized that after I posted- here is a snapshot of the RAM memory usage, for what it’s worth.

The output seems to be there nevertheless, despite that error. I will check out the Software Support template.

Thank you so much!
Lavinia

5

Hi @lavinia.carmen.u,

I’d suggest upgrading to a newer version, as 23.2.1 is a bit outdated. Also how are you setting your memory limit for neurodesk? It’s also possible that your RAM limit of 12GB is not enough. Have you tried just running a single BOLD file, i.e., by using a --bids-filter-file?

Best,
Steven

6

The last fmriprep version I see in Neurodesk is 23.2.1, but I could try to get a newer one.
I haven’t tried on a single BOLD file yet, but will try that next.
I also haven’t set the memory limit - will look into that as well.
Thank you for the suggestions!