[Mne_analysis] Problem including reference electrode in info['chs'][.]['loc']

[Emily Stephen]

Hi Again,

I've been debugging my code by comparing an EEG forward model that I
constructed using MNE python to one constructed by a former labmate using
MNE C. The lead field matrices are different, even when I use identical
source space, BEM solution, and transformation file.

I've narrowed down the problem to info['chs'][...]['eeg_loc'], which in the
old data is 3x2, with the second column having the location of the
reference electrode. In my data, eeg_loc is 3x1, with no information about
the location of the reference electrode. The information in this second
column appears to be used by _bem_specify_els, which loops over the columns
of the electrode location matrix.

I've played around a bit with add_reference_channels and set_eeg_reference,
but neither of them changes the second column in eeg_loc for the
non-reference electrodes. The location of the reference electrode is
specified in my montage file (hpts), but there doesn't seem to be a way to
apply it to the eeg_loc of all of the other electrodes.

This is what I thought might have worked, but it seems to just add another
electrode, without influencing the chs of the other electrodes:
montage = mne.channels.read_montage(montage_hpts, transform=True, unit='mm')
raw = mne.io.read_raw_fif(rawfile,preload=True)
mne.io.add_reference_channels(raw,'EEG000',copy=False)
raw.set_montage(montage)
mne.io.set_eeg_reference(raw,['EEG000'],copy=False)

Thoughts?

Thanks,
Emily
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