[Mne_analysis] Relevance of Freesurfer expert settings for MNE workflow

[dgw]

Hi Denis,

Well, I'm not sure what you mean by "expert settings". In my
experience, as long as your FreeSurfer white matter surfaces look good
(based on experience with the FreeSurfer Tutorial) and your BEM
surfaces look good (most important for EEG), your results should be
robust. Importantly, at least at the moment the pial surfaces are not
used in MNE, so editing them does not affect the inverse solution.
Obviously optimizing your MR acquisition for the highest quality
possible will improve FreeSurfer's performance (the biggest effect I
have noticed is in reduced manual editing necessary).

The most concerning errors (outside of obvious problems e.g. missing
lobes etc) are those where the surface becomes "sharp". This geometry
will yield strange influences in your estimates and also is
physiologically unlikely. Another important consideration is
decimation (whether you do, and how you do), furthermore, I strongly
recommend using --loosevar with any decimated data.

HTH
D

On Wed, Oct 10, 2012 at 7:08 AM, Denis-Alexander Engemann
<d.engemann at fz-juelich.de> wrote:
> Dear MNEs,
>
> I just learned about the possibility that the Freesurfer segmentation
> quality could depend on the set of imaging parameters used.
> For my current measurements I have access to mprages measured on a 3T
> Siemens Trio device with a 16-Ch coil.
> The segmentation looks ok and also my source estimates, but I was
> wondering whether the passing expert settings instead of the defaults
> when invoking recon-all should make a practically significant
> difference.
> Does anyone have experience with this?
>
> Cheers,
> Denis
>
>
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