Passing `trans` to mne.gui.coregistration() should automatically derive the MRI fiducials

Currently, the following code will estimate the fiducials from fsaverage and ask me to (re)place them; however, with a trans provided, deriving the MRI fiducials is very easy and is actually what I’d expect to be done automatically. I shouldn’t have to pick fiducials again if a trans has already been generated!

import os.path as op
import mne
from mne.io import read_info

data_path = mne.datasets.sample.data_path()
subjects_dir = op.join(data_path, 'subjects')
subject = 'sample'

fname_raw = op.join(data_path, 'MEG', subject, subject + '_audvis_raw.fif')
fname_trans = op.join(data_path, 'MEG', subject, 
                      f'{subject}_audvis_raw-trans.fif')

mne.gui.coregistration(
    subject='sample',
    subjects_dir=subjects_dir,
    inst=fname_raw,
    trans=fname_trans,
)

cc @GuillaumeFavelier

[larsoner]

We do not have a way to specify the path to load the fiducials in the command line with mne coreg right?

Correct, and YAGNI. The standard location SUBJECTS_DIR/SUBJECT/bem/SUBJECT-fiducials.fif should be enough in 99% of cases.

[larsoner]

@GuillaumeFavelier Looking at the code, I believe the fiducials file is currently saved automatically once the fiducials have been placed, is this correct?

When I’ve run mne coreg multiple times with -s sample, it goes into fiducial-editing mode on startup every time. So it either isn’t saving it (to the right place), or it’s not detecting the presence of sample/bem/sample-fiducials.fif.

FWIW I don’t think it should auto-save – I think there should be a save button, the filename field should auto-populate with $SUBJECTS_DIR/$SUBJECT/bem/$SUBJECT-fiducials.fif, and if you click “save” and the file exists, you should get a popup prompt asking if you’re sure you want to overwrite. (This is one case where a file browser could potentially be used, but we really want people to stick with the standard filename so I’d rather not tempt them to use something else by making browsing/selecting something different easier.)