Q: CTF coregistration with separate coil position?

Problem

I am trying to coregister CTF data with an MRI to produce a -trans.fif

What I have

The MEG data is separate from the positions in digitizer space so the raw file doesn’t know about: hpi_coils.txt, head_shape.txt, fiducials.txt.

The HPI coil positions in MEG device space seem to be stored in the raw file: 'dig_points' and 'coord_trans' are present in raw.info['hpi_results'] after reading the raw.

Where I was going

I thought I would

1. create a mne.channels.DigMontage from this data (I am just unsure whether raw.info['hpi_results'][0]['coord_trans'] corresponds to the parameter 'dev_head_t' required by DigMontage).
2. apply this montage to my raw file using raw.set_montage(my_new_montage).save(raw_fname).

Where I’m stuck

However, mne.gui.coregistration still does not show the head shape positions nor the HPI coils.

Any idea how to proceed?

(For the KIT, thanks to @teonbrooks, this is handle at the reading stage (read_raw_kit needs the headshape to create the raw), and in the Elekta the position are in the raw.fif in the first place.)

[romquentin]

Ok. Thanks again!

[kingjr]

Thanks @LauraGwilliams !

@romquentin: @teonbrooks and I met and manage to incorporate the HPI, fiducials and digitized head shape points in an MNE object: https://gist.github.com/kingjr/8f971c73c79712b547cdd55c661c6a5a

you need to :

• write a parser to extract the HPI, head shape and fiducials as numpy arrays similar to what is in the gist.
• duplicate your HPI, as the read_dig_montage expect hpi points that are called lpa, rpa and nasion for the coordinates transformation, and will use the other as hpi coils.
• save your mne object on the hard drive as mne.gui.coregistration expects a file and not an mne instance directly.

If you’re ok, I’ll close the issue.