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

[Marijn van Vliet]

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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