[Mne_analysis] Import BEM model from fieldtrip to MNE

[Edoardo Pinzuti]

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Hi Eric,

thanks this help.  Only one question for my understanding. *Is* the
brainmask.mgz  used by the watershed algorithm at all ?

Il giorno lun 27 apr 2020 alle ore 22:45 Eric Larson <
larson.eric.d at gmail.com> ha scritto:

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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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