--use-syn-sdc no longer respected when --ignore fieldmaps is passed

[effigies]

Prior to 1.5.3, --use-syn-sdc --ignore fieldmaps would ignore fieldmaps, and use SyN-SDC.

As of 9e23203 (#1886), access to any SDC algorithm is restricted by --ignore fieldmaps.

This leaves users who would prefer to use SyN over fieldmaps stranded.

Ref: https://neurostars.org/t/syn-sdc-not-working-with-more-recent-fmriprep-version/5824

[effigies]

This appears to still occur in 20.1.0rc1.

[effigies]

From the reports:

Functional

Reports for: task repeatchange, run 1.

Summary

• Repetition time (TR): 3.38s
• Phase-encoding (PE) direction: Anterior-Posterior
• Slice timing correction: Not applied
• Susceptibility distortion correction: None

...

About

fMRIPrep version: 20.1.0rc1
fMRIPrep command: /usr/local/miniconda/bin/fmriprep sourcedata/ . participant --participant-label 02 --output-spaces anat fsnative --cifti-output --ignore fieldmaps --use-syn-sdc -vv --fs-license-file /projectnb/bohland/repeat_change/worktrees/02/tokens/freesurfer_license.txt --nthreads 16 --omp-nthreads 8 --mem-mb 48000
Date preprocessed: 2020-04-09 21:45:06 -0400

[effigies]

@oesteban Could this be because the CLI flag is --use-syn-sdc, and the new config variable is use_syn?

https://github.com/poldracklab/fmriprep/blob/549e7876c8ffdfd2a2472d22cb3dcf3c0d22fab7/fmriprep/cli/parser.py#L234-L235

https://github.com/poldracklab/fmriprep/blob/549e7876c8ffdfd2a2472d22cb3dcf3c0d22fab7/fmriprep/config.py#L459-L461

Or do we account for this mismatch somewhere?

[mgxd]

@effigies that seems like the case - I'll double check the config options to see if there are any other deviations from the parser