Read-only file system error - fmriprep

I’m running fmriprep using Docker containers on a computer running Windows 10. WSL 2 is enabled. It runs great for about 7-8 hours before crashing (which is very frustrating in terms of debugging).

Here is the command I run:

fmriprep-docker E:/BIDS/Project/Nifti E:/BIDS/Project/derivatives participant --participant-label 01 --fs-license-file E:/BIDS/Project/freesurfer_license.txt

Here is the error message from the crash logfile it outputs:

Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/”, line 344, in _send_procs_to_workers
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/”, line 520, in run
if not silentrm(hashfile_unfinished):
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/utils/”, line 818, in silentrm
OSError: [Errno 30] Read-only file system: ‘/tmp/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_03_task_test_run_1_wf/func_derivatives_wf/_in_tuple_MNI152NLin2009cAsym.resnative/ds_bold_std/_0x1d358297a6b82b5208430d8e05abca84_unfinished.json’

So I’m guessing it’s something to do with the read/write file permissions? Does anyone have any other insights into this issue? Let me know if any other information would be helpful. I appreciate the help!

I would guess you’re running out of space, and it exhibits weirdly in Docker. Try passing in a working directory with -w.

You were right, it was a space error on my C: drive. Thanks!

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