[Mne_analysis] Coregistration

[Alexandre Gramfort]

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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