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 (
mne.scale_bem — MNE 1.6.0 documentation)
to scale the bem for your already existing scaled brains.
Christian
>
> 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
>
>> 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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