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

[Mainak Jas]

Hi Emily,

I think some other developer might be better suited to answer your full
question. But are you by any chance looking for raw.apply_proj()?

Best regards,
Mainak

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

> Yes. Well, in the old data the average reference projector's active
> property is set to 'on', and in my data it is set to 'off'.
>
> I tried running mne.io.proj.activate_proj to make it active in the new
> data, and it did not affect the lead field matrix. Is there some other way
> to activate the proj?
>
> Emily
>
> On Thu, Dec 10, 2015 at 5:30 PM, Hari Bharadwaj <hari at nmr.mgh.harvard.edu>
> wrote:
>
>> Hi Emily,
>>     My immediate thought is.. do you have an average reference projector
>> that is being applied in one case and not the other?
>>
>> Hari
>>
>> On Thu, December 10, 2015 5:25 pm, Emily Stephen 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
>> > _______________________________________________
>> > Mne_analysis mailing list
>> > Mne_analysis at nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>>
>> --
>> Hari Bharadwaj
>> Research Fellow
>> Martinos Center for Biomedical Imaging,
>> Massachusetts General Hospital
>> 149 Thirteenth Street,
>> Charlestown, MA 02129
>>
>> hari at nmr.mgh.harvard.edu
>> Ph: 734-883-5954
>> www.haribharadwaj.com
>>
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