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

Hari Bharadwaj hari at nmr.mgh.harvard.edu
Thu Dec 10 17:30:50 EST 2015
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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
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-- 
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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