[Mne_analysis] Coregistration

[Christian Brodbeck]

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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