<div dir="ltr"><div>Thank you all for help!</div><div><br></div><div>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?</div><div><br></div><div>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? </div><div><br></div><div>Thanks so much.</div><div><br></div><div>Mengting</div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">2014-10-31 10:25 GMT-04:00 Christian Brodbeck <span dir="ltr"><<a href="mailto:christianbrodbeck@nyu.edu" target="_blank">christianbrodbeck@nyu.edu</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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 (<a href="http://martinos.org/mne/stable/generated/mne.scale_bem.html#mne.scale_bem" target="_blank">http://martinos.org/mne/stable/generated/mne.scale_bem.html#mne.scale_bem</a>) to scale the bem for your already existing scaled brains.<br>
<span class="HOEnZb"><font color="#888888"><br>
Christian<br>
</font></span><div class="HOEnZb"><div class="h5"><br>
<br>
> On Oct 31, 2014, at 7:04, Alexandre Gramfort <<a href="mailto:alexandre.gramfort@telecom-paristech.fr">alexandre.gramfort@telecom-paristech.fr</a>> wrote:<br>
><br>
> maybe Christian can comment but to me you should first compute the BEM<br>
> model for average brain and then scale it. So you call<br>
> mne_watershed_bem only once on your template.<br>
><br>
> HTH<br>
> Alex<br>
><br>
> On Thu, Oct 30, 2014 at 7:22 PM, Liu Mengting <<a href="mailto:bigting84@gmail.com">bigting84@gmail.com</a>> wrote:<br>
>> Thanks, but then I have another question, after I co-registered using<br>
>> mne.gui.coregistration, I need a 3-layer BEM for EEG forward modeling,<br>
>> Usually I use mne_watershed_bem to create one with the infomation in<br>
>> template brain, but I cannot find the any MRI files in the brain/subject<br>
>> folder I scaled, thus I am not able to make a BEM using the brain I<br>
>> coregistered, can you let me know how to use the co-registered brain to make<br>
>> 3-layer BEM please?<br>
>><br>
>> Thanks,<br>
>><br>
>> Mengting<br>
>><br>
>> 2014-10-30 4:21 GMT-04:00 Alexandre Gramfort<br>
>> <<a href="mailto:alexandre.gramfort@telecom-paristech.fr">alexandre.gramfort@telecom-paristech.fr</a>>:<br>
>><br>
>>> hi,<br>
>>><br>
>>>> I have a basic question about coregistration in EEG forward modeling<br>
>>>> using<br>
>>>> fsaverage brain, when I tried to align the EEG channels and fMRI by<br>
>>>> mne.gui.coregistration, it seems to scale the head shape to fit the<br>
>>>> electrode;<br>
>>><br>
>>> this is correct.<br>
>>><br>
>>>> but when I made the alignment using mne_analyze, it seems to move<br>
>>>> and scale the electrodes to fit the head shape. So are these two way the<br>
>>>> same?<br>
>>><br>
>>> mne_analyze does not support template brains. So it does not<br>
>>> scale anything but just find the best translation+rotation to fit the<br>
>>> scalp surface<br>
>>> to the electrode positions.<br>
>>><br>
>>> Alex<br>
>>><br>
>>>> Also, when I set fiducials in mne_analyze, the coordinates of<br>
>>>> LAP/NASION/RAP will always have a 400 mm (which was definitly wrong)when<br>
>>>> I<br>
>>>> clicked on where I want to set the fiducials on the head surface, and I<br>
>>>> also<br>
>>>> am not able to type in the coordinates by hand, does it sound correct?<br>
>>>><br>
>>>> thanks,<br>
>>>><br>
>>>> Mengting<br>
>>>><br>
>>>><br>
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