Summary of what happened:
I am trying to run fmriprep on neuroimaging data from 20 participants. My BIDS-validated dataset consists of a T1 image, reverse phase encoding field maps, and 4 task-based BOLD runs.
I ran fmriprep on just a single participant to begin with, in order to more easily troubleshoot any issues that arose. The process was terminated, and a few crash reports were generated. I repeated this process for other participants and similar (but not always exactly the same) crash reports were provided.
I would appreciate if anyone is able to help me interpret these crash reports to find the most likely root cause(s). When simply passing the reports through ChatGPT, it suggests that there could be an issue with insufficient memory on the cluster server on which fmriprep is being run. Could someone help me to confirm whether I am indeed encountering a server-related problem, as opposed to an fmriprep- or data-related problem?
Thank you!
Alex
Command used (and if a helper script was used, a link to the helper script or the command generated):
I have attached the crash reports, as well as my .sh script for running fmriprep, in the following WeTransfer link: Unique Download Link | WeTransfer.
Version:
fmriprep version 23.2.2.
Environment (Docker, Singularity / Apptainer, custom installation):
I am running fmriprep on our university’s HPC cluster server. I have a singularity image in the appropriate directory which corresponds to the fmriprep version that I am using. The code for running fmriprep is contained within a .sh script which I run from the terminal of the HPC server.
Data formatted according to a validatable standard? Please provide the output of the validator:
I have also attached the BIDS Validator error log to the same WeTransfer link as above: Unique Download Link | WeTransfer.
Relevant log outputs (up to 20 lines):
Frustratingly, log outputs are not always created from my fmriprep sessions. I only receive crash reports.