argument --slice-time-ref: invalid _slice_time_ref value: '0'

[bmelo]

Hi all, we are trying to run the new fMRIPrep 20.2.4 release to use the new flag --slice-time-ref, but we are getting the following errors:

fmriprep: error: argument --slice-time-ref: invalid _slice_time_ref value: 'start'
fmriprep: error: argument --slice-time-ref: invalid _slice_time_ref value: '0'

It seems that the argument is wrong, but accordingly to the code it seems fine. Are we doing something wrong?

What version of fMRIPrep are you using?

20.2.4

What kind of installation are you using? Containers (Singularity, Docker), or "bare-metal"?

Singularity

What is the exact command-line you used?

fmriprep-20.2.4.sif --slice-time-ref 0 $BIDSDIR $OUTPUTDIR participant --participant_label $SUBJID

and

fmriprep-20.2.4.sif --slice-time-ref start $BIDSDIR $OUTPUTDIR participant --participant_label $SUBJID

Have you checked that your inputs are BIDS valid?

Yes.

Did fMRIPrep generate the visual report for this particular subject? If yes, could you share it?

No.

Can you find some traces of the error reported in the visual report (at the bottom) or in crashfiles?

fmriprep: error: argument --slice-time-ref: invalid _slice_time_ref value: '0'

Are you reusing previously computed results (e.g., FreeSurfer, Anatomical derivatives, work directory of previous run)?

No.

fMRIPrep log

If you have access to the output logged by fMRIPrep, please make sure to attach it as a text file to this issue.

It's not starting.

[effigies]

Thanks for this. I'm able to reproduce the issue in tests. Will see what's up.

[mgxd]

I think the problem is

fmriprep/fmriprep/cli/parser.py

Line 70 in 5fe2c33

def _slice_time_ref(value, parser):

needs to be converted to a partial to be used as an argparse type, since it requires the parser object.

[effigies]

Yup. I didn't realize that was our own hack. Submitting a PR now.

[effigies]

Closed by #2573.