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

[Emily Stephen]

I think the code works properly if the eeg_loc is set to the correct 3x2
matrix: I reran the forward solution for the old data using MNE python and
I get basically the same answer as MNE C (differences on the order of
10^-3, when the lead field matrix entries are on the order of 100). So MNE
python is loading the data properly and using it properly.

The problem is that I can't create a Raw object using *only* MNE python
that has the supposedly correct 3x2 eeg_loc parameters. I think the
solution would involve adding the reference electrode to the Montage or the
DigMontage, since that's where the information is (at least in my data). In
case it matters, I'm getting my Montage from a hpts file that labels the
reference as eeg electrode 0. Since that electrode doesn't exist in the
recordings, it isn't used by set_montage. That's why I thought it might
work to add the reference electrode using add_reference_channels before
running set_montage.

Emily



On Fri, Dec 11, 2015 at 10:22 AM, Emily Stephen <emilyps14 at gmail.com> wrote:

> 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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