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

[Emily Stephen]

One more thing: the only place in the documentation that talks about the
reference channel location being stored with eeg channel locations is here:
http://martinos.org/mne/stable/manual/c_reference.html
under the entries for "ch_pos" in the matlab structures.

I'm assuming ch_pos in the matlab structures serves the same purpose as
eeg_loc in the python info dicts.

Emily

On Fri, Dec 11, 2015 at 10:34 AM, Emily Stephen <emilyps14 at gmail.com> wrote:

> 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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>>
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