Hanging on `fsnative2t1w_xfm`

[joey-scanga]

Describe the bug

Please correct me if this isn't permitted, but I'm crossposting from nipreps/fmriprep#3562 since there hasn't been any responses to that issue yet.

I'm consistently experiencing hanging in fmriprep when running with the --fs-no-resume flag whenever it reaches smriprep's fsnative2t1w_xfm node.

Exact command line executed

docker run --rm -it -u 2582:10 \
    -v /usr/local/pkg/freesurfer7.3/.license:/opt/freesurfer/license.txt:ro \
    -v /data/sylvester/data1/datasets/spc_new/rawdata:/data:ro \
    -v /data/sylvester/data1/datasets/spc_new/derivatives/fmriprep:/out \
    -v /data/sylvester/scratch1/spc_new/fmriprep/sub-SPC026_ses-01:/work \
    -v /data/sylvester/data1/datasets/spc_new/derivatives/fmriprep/sourcedata/freesurfer:/deriv1 \
    nipreps/fmriprep:25.2.2 \
    /data /out participant \
    --participant-label SPC026 \
    -w /work \
    --verbose \
    --fs-subjects-dir /deriv1 \
    --fd-spike-threshold 0.9 \
    --fs-no-resume \
    --cifti-output 91k \
    --output-spaces MNI152NLin2009cAsym

Are you positive that the input dataset is BIDS-compliant?

• I have used the online BIDS-Validator
• I have run a local installation of the BIDS-Validator (please, note the version of the validator here).
  Whichever version used in fmriprep 23.2.2 (the Dockerfile implies this is 1.14.10)
• I let sMRIPrep check it for me (in other words, I didn't set the --skip-bids-validation argument).
• No, I haven't checked myself AND used the --skip-bids-validation argument.

sMRIPrep feedback information
Please attach the full log written to the standard output and the crashfile(s), if generated.

Visual reports of sMRIPrep
If applicable, add screenshots or attach the corresponding "reportlets" to help explain your problem.

Installation type (please complete the following information):

• "Bare-metal"
• Singularity
• Docker

Additional context
Add any other context about the problem here.

Here's a screenshot of where fmriprep hangs at.

[effigies]

When you look at top or similar, are you seeing a mri_robust_register process running? If not, there's probably an error higher up in the log that crashed out fsnative2t1w_xfm.

[joey-scanga]

Good question... I'll have to run another instance and see, our filesystem is down atm but I'll update as soon as I can. Thanks!!