[Mne_analysis] Trans file without digitized data (Florian Aspart)

[Florian Aspart]

Hi all,

thank you a lot for your answer and sorry for the response delay, I first
wanted to try your suggestion before coming back to you.

@Alex: this is what I want to do: rescale the fsaverage BEM model using the
coreg GUI to fit the standard montage with electrodes constrained on a
sphere. But I do not know how to create the digitized points coordinates
for these electrode.

@Marina: your answer helped me going towards the right direction.
Nevertheless, I could not get it to work correctly.
I created the  raw.info['dig'] structure as you suggested but when I use it
in the coregistration GUI, I get far too high fiducials errors:
"LPA: 137548.5mm, NAS: 0.0mm, RPA: 171781.1 mm"
I guess the fiducials positions I read in the  standard montage are not in
the correct coordinate system or do not have the correct scaling.
Could you maybe share the code you are using to create the dig structure?
Do you get plausible results for the source reconstruction using this
technique?

Best,
Florian




> ---------- Message transféré ----------
> From: "Saiz Alía, Marina" <marina.saiz-alia15 at imperial.ac.uk>
> To: "mne_analysis at nmr.mgh.harvard.edu" <mne_analysis at nmr.mgh.harvard.edu>
> Cc:
> Date: Fri, 16 Sep 2016 08:23:28 +0000
> Subject: [Mne_analysis] 3. Trans file without digitized data (Florian
> Aspart)
> Hello Florian,
>
> I do source reconstruction with EEG 64 channels and using fsaverage
> average brain from FreeSurfer too.
>
> I had the same problem. I was trying to get the trans file using mne coreg
> but my EEG data did not have the dig points. So what I did is to use the
> standard 10-20 electrode positions that I read using montage function, when
> loading the data.
>
> I copied the positions of the EEG channels and the fiducial points into
> the raw.info[‘dig’] structure, saved the new raw file as .fif and then
> when I loaded it in mne correg I would see the digitized points over the
> fsaverage brain I previously selected.
>
> Let me know if you don’t know how to do it and I will try to help you but
> basically you just need to copy the positions into this info structure.
> Make sure LPA, RPA and nazion are ordered as dig structure requieres, just
> in case. You can load mne sample data set and check how this raw.info[‘dig’]
> structure has to be.
>
> Hope it helps although if you need more help I can send you my code or try
> to be more specific. I am not in the office now and I don’t exactly
> remember how I did it. But it is basically what I am telling you now.
>
> Marina.
>
> ---------- Message transféré ----------
> From: Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr>
> To: Discussion and support forum for the users of MNE Software <
> mne_analysis at nmr.mgh.harvard.edu>
> Cc:
> Date: Mon, 19 Sep 2016 13:32:03 +0200
> Subject: Re: [Mne_analysis] Trans file without digitized data
> hi Florian,
>
> use a standard montage with electrodes constrained on a sphere. If you want
> to use a BEM model you need to rescale fsaverage. The coreg GUI in mne
> -python
> allows you to do this AFAIK.
>
> HTH
>
> Alex
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