Summary of what happened:
I’m was trying to run fmriprep on win10 via docker with specified --output-space T1w flag but get an error that is due to a failure in accessing a directory / file that ends with a “.” which i assume could not be properly created in the first place as windows omits the “.” at the end. The directory exists without the “.” and is empty.
Previously i successfully ran fmriprep on the same data but did not specify any output spaces (i.e. standard MNI152NLin2009cAsym) which worked like a charm. The error persists when specifying other non-standard spaces. I used fmriprep 21.0.2 here (to match the previous run) but it also doesn’t work for the latest version (22.0.2).
docker run -ti --rm -v path/to/nifti:/data -v path/to/derivatives:/out -v path/to/workdir:/work -v path/to/fslicense:/licensePath nipreps/fmriprep:21.0.2 /data /out/fmriprep participant --participant-label 01 -w /work --output-space T1w --stop-on-first-crash --fs-license-file /licensePath/freesurfer.txt
21.0.2 but also with latest version of fmriprep
Environment (Docker, Singularity, custom installation):
Data formatted according to a validatable standard? Please provide the output of the validator:
This dataset appears to be BIDS compatible.
Relevant log outputs (up to 20 lines):
230220-10:32:51,994 nipype.workflow ERROR: Saving crash info to /out/fmriprep/sub-01/log/20230220-102810_39d36581-9bc2-4a40-8b6f-9a1ca4ae6719/crash-20230220-103251-root-split_target.a0-f7845e58-629a-47eb-8c8a-ce0e7775b7c5.txt Traceback (most recent call last): File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers self.procs[jobid].run(updatehash=updatehash) File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 507, in run os.makedirs(outdir, exist_ok=True) File "/opt/conda/lib/python3.8/os.py", line 223, in makedirs mkdir(name, mode) FileNotFoundError: [Errno 2] No such file or directory: '/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_encoding_run_04_wf/bold_std_trans_wf/_std_target_MNI152NLin2009cAsym./split_target'
Screenshots / relevant information:
something very similar has been discussed [here] ("." being replaces by unicode symbo in `anat_norm_wf` node `split_desc.aI.a0` · Issue #1944 · nipreps/fmriprep · GitHub):
and [here] (fmriprep trying to create folder that ends with a dot in its name in Windows? · Issue #2046 · nipreps/fmriprep · GitHub): but in my case the error persist when specifying output spaces, not when omitting them and generating the standard output.