[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
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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