Summary of what happened:
Hey everyone,
I’m encountering a persistent problem with fMRIPrep, and I’m hoping someone here might be able to help me troubleshoot it. The process crashes during the BOLD correction step, specifically at the node bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask.
- I’ve verified the integrity of the input files using the BIDS Validator.
- I’ve also checked the permissions to ensure that Docker has read/write access to the directories.
Despite all this, the process consistently fails at the same step. When I was searching about this, I came across to these resources Fmriprep crash wf.initial_boldref_wf.enhance_and_skullstrip_bold_wf.n4_correct how to become an aws devops engineer and as per them I tried the following-
- Re-downloading Data
- Attempted to run fMRIPrep on a different machine with similar specifications, but encountered the same error.
- Ensured that I’m using the latest version of fMRIPrep, but the problem remains unchanged.
- I’ve looked through the log files, but haven’t found any additional clues that could point to the root cause.
I’m at a bit of a loss here and would really appreciate any insights or suggestions on how to resolve this issue. Has anyone else faced a similar problem or could point me in the right direction? Are there any specific configurations or steps I might be missing?
Thank you so much for your time and assistance!
Best Regards 
Command used (and if a helper script was used, a link to the helper script or the command generated):
docker run -ti --rm \
-v /bids_dataset:/data:ro \
-v /outputs:/out \
poldracklab/fmriprep:latest \
/data /out participant \
--participant_label 01 \
--fs-license-file /path/to/license.txt
Version:
poldracklab/fmriprep:latest
Environment (Docker, Singularity / Apptainer, custom installation):
- OS: Ubuntu 20.04
- Docker version: 20.10.7
- Memory: 32GB RAM
- CPU: Intel Core i7-9700K
Data formatted according to a validatable standard? Please provide the output of the validator:
I have organized my BIDS dataset following the standard format. The directory structure is as follows:
/bids_dataset
├── sub-01
│ ├── anat
│ │ └── sub-01_T1w.nii.gz
│ └── func
│ └── sub-01_task-rest_bold.nii.gz
├── dataset_description.json
├── participants.tsv
└──
...
Relevant log outputs (up to 20 lines):
Node Name: bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask
Error Message: No such file or directory: '/out/fmriprep/sub-01/func/sub-01_task-rest_bold_space-T1w_preproc.nii.gz'