[Mne_analysis] Coregistration

Liu Mengting bigting84 at gmail.com
Tue Nov 4 01:04:07 EST 2014
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Thank you all for help!

I've tried to use mne.scale_bem to scale the 3 layer bem-sol file but not
successful, so I suppose that I need to first make a 3-layers -bem file,
then scale it using mne.scale_bem, and then use the scaled -bem file to
make a bem-sol file right?

In my study, I have only EEG data from biosemi and standard electrode
location files, and I want to do the source localization in a template
brain. When I use EEGlab or BESA, they all try to adjust/warp the standard
sensor locations to fit the template head shape. But in MNE, I need to
scale the head as well as all their related bem files and labels to
continue the forward modeling. It looks far more complicated than the
former way, I am just wondering is there any way similar (and maybe easier)
in MNE for EEG sensor alignment in a template brain?

Thanks so much.

Mengting



2014-10-31 10:25 GMT-04:00 Christian Brodbeck <christianbrodbeck at nyu.edu>:

> Exactly, when you scale an MRI any bem file with a path corresponding to
> bem/{subject}-*-bem.fif should also be scaled. If you already scaled your
> brains you can create the bem for fsaverage and then use mne.scale_bem (
> http://martinos.org/mne/stable/generated/mne.scale_bem.html#mne.scale_bem)
> to scale the bem for your already existing scaled brains.
>
> Christian
>
>
> > On Oct 31, 2014, at 7:04, Alexandre Gramfort <
> alexandre.gramfort at telecom-paristech.fr> wrote:
> >
> > maybe Christian can comment but to me you should first compute the BEM
> > model for average brain and then scale it. So you call
> > mne_watershed_bem only once on your template.
> >
> > HTH
> > Alex
> >
> > On Thu, Oct 30, 2014 at 7:22 PM, Liu Mengting <bigting84 at gmail.com>
> wrote:
> >> Thanks, but then I have another question, after I co-registered using
> >> mne.gui.coregistration, I need a 3-layer BEM for EEG forward modeling,
> >> Usually I use mne_watershed_bem to create one with the infomation in
> >> template brain, but I cannot find the any MRI files in the brain/subject
> >> folder I scaled, thus I am not able to make a BEM using the brain I
> >> coregistered, can you let me know how to use the co-registered brain to
> make
> >> 3-layer BEM please?
> >>
> >> Thanks,
> >>
> >> Mengting
> >>
> >> 2014-10-30 4:21 GMT-04:00 Alexandre Gramfort
> >> <alexandre.gramfort at telecom-paristech.fr>:
> >>
> >>> hi,
> >>>
> >>>> I have a basic question about coregistration in EEG forward modeling
> >>>> using
> >>>> fsaverage brain, when I tried to align the EEG channels and fMRI by
> >>>> mne.gui.coregistration, it seems to scale the head shape to fit the
> >>>> electrode;
> >>>
> >>> this is correct.
> >>>
> >>>> but when I made the alignment using mne_analyze, it seems to move
> >>>> and scale the electrodes to fit the head shape. So are these two way
> the
> >>>> same?
> >>>
> >>> mne_analyze does not support template brains. So it does not
> >>> scale anything but just find the best translation+rotation to fit the
> >>> scalp surface
> >>> to the electrode positions.
> >>>
> >>> Alex
> >>>
> >>>> Also, when I set fiducials in mne_analyze, the coordinates of
> >>>> LAP/NASION/RAP will always have a 400 mm (which was definitly
> wrong)when
> >>>> I
> >>>> clicked on where I want to set the fiducials on the head surface, and
> I
> >>>> also
> >>>> am not able to type in the coordinates by hand, does it sound correct?
> >>>>
> >>>> thanks,
> >>>>
> >>>> Mengting
> >>>>
> >>>>
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