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

[Emily Stephen]

In line 141, _bem_specify_els loops over the columns of el_r, which is a
transformed version of els[...][rmag].

els comes from the coils variable in _prep_field_computation, which come
from fwd_data from _compute_forwards, yada yada yada...

If you trace it all the way to its source, the field rmag is set through
make_forward_solution > _prep_channels > _create_coils > _create_eeg_el,
which sets it to a (potentially transformed) version of ch[eeg_loc].

The reason it matters is that in _bem_specify_els, the sol variable is
constructed as a weighted sum of the bem solution at tri vertices near the
locations in the columns of rmag. The weight w on the second column (from
elw, also set in _create_eeg_el) is -1. So the bem is subtracting off the
influence of the reference electrode.

Apologies if this is vague -- I'm still familiarizing myself with the
theory. At this point I have a better grasp on the code, since I've been
stepping through it debugging.

Thanks,
Emily

On Fri, Dec 11, 2015 at 2:32 AM, Marijn van Vliet <w.m.vanvliet at gmail.com>
wrote:

> Dear Emily,
>
> the `set_eeg_reference` and `add_reference_channels` are functions that
> transform the EEG data. They allow you to specify different referencing
> schemes, which is useful for sensor level analysis. They also set the
> `custom_ref_applied` flag in the info structure to explicitly override the
> average reference projector. Since you are doing source localisation and
> therefore want the average reference, don’t use these functions, they don’t
> do what you wanted them to do.
>
> Let’s move on to your problem:
>
> I was always wondering why `eeg_loc` was a 3x2 matrix… thank you for
> tracking it down. I think many of our data import routines only set the
> first row of `eeg_loc`; this should be fixed. However, where in
> `_bem_specify_els` does it loop over the `eeg_loc` matrix exactly? I can’t
> find it...
>
> regards,
> Marijn.
> --
> Marijn van Vliet
> w.m.vanvliet at gmail.com
>
>
>
>
>
> > On 11 Dec 2015, at 00:25, Emily Stephen <emilyps14 at gmail.com> wrote:
> >
> > 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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