[Mne_analysis] Import BEM model from fieldtrip to MNE

Eric Larson larson.eric.d at gmail.com
Mon Apr 27 16:44:22 EDT 2020
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You can run FreeSurfer in discrete steps and correct the brainmask.mgz at
the right point in the processing (probably at the end of -autorecon1). See:

https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable

See also "going farther back" here:

https://mne.tools/dev/overview/faq.html#my-watershed-bem-meshes-look-incorrect

Alternatively, if you don't want to mess with FreeSurfer, you could try
dealing with the coordinate frames and such. Usually looking at the output
of `plot_alignment` with the subject/src/trans/bem set properly (and also
plot_bem) will tell you if the forward calculation will do what you want it
to do. See for example:

https://mne.tools/dev/auto_tutorials/source-modeling/plot_forward.html

Eric



On Mon, Apr 27, 2020 at 4:39 PM Edoardo Pinzuti <edoardo.pinzuti at gmail.com>
wrote:

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>
> The only problem is that the FreeSurfer skullstripping and other
> segmentation steps do not work well (maybe due to a not so good T1) and it
> required  manual correction. On the other hand, I have the corrected brain
> mask. Could be one solution to run FreeSurfer with  this brainmask?
>
> Thanks a lot
>
> Il giorno lun 27 apr 2020 alle ore 22:23 Alexandre Gramfort <
> alexandre.gramfort at inria.fr> ha scritto:
>
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>> I would redo the segmentation as it will be just a few hours of CPU time
>> and you're sure not to mess it up with coord frames etc.
>>
>> my 2c
>> Alex
>>
>>
>> On Mon, Apr 27, 2020 at 6:17 PM Edoardo Pinzuti <
>> edoardo.pinzuti at gmail.com> wrote:
>>
>>>         External Email - Use Caution
>>>
>>> Dear MNE experts,
>>>
>>> I have already done a year ago  the segmentation and the BEM models  in
>>> fiedltrip. Is there a way  to import them in MNE without starting  from the
>>> segmentation again ?
>>>
>>> Thanks
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