[Mne_analysis] Import BEM model from fieldtrip to MNE

[Eric Larson]

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It might not be -- it might be recomputed by the `watershed` code. I'm not
sure, though, you'd have to ask the Freesurfer folks how it actually works.

Eric


On Tue, May 26, 2020 at 6:39 AM Edoardo Pinzuti <edoardo.pinzuti at gmail.com>
wrote:

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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:
>
>>         External Email - Use Caution
>>
>> 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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