[Mne_analysis] Correspondence of source space with parcellation : another doubt ...

thierry nieus thierry.nieus at unimi.it
Fri Sep 13 08:38:33 EDT 2019
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Hi Eric,
thanks a lot for the clarification. The last days I went also though the
mailing list and found a "patch" to the problem of matching the sources
with the lobes.
For the convenience of other users with similar issues I post the direct
link to it:

Fill missing vertices in parcellation and save the labels

https://mail.nmr.mgh.harvard.edu/pipermail//mne_analysis/attachments/20140818/2347751d/attachment.py

Best



On Fri, Sep 6, 2019 at 4:00 PM Eric Larson <larson.eric.d at gmail.com> wrote:

>         External Email - Use Caution
>
> I am still stuck with the correspondence of the source space with
>> parcellation.
>>
>
> In general, a source space takes the high resolution mesh (~100k verts)
> and subselects a small subset of them (~10k or less). The subset is stored
> in `src[0]['vertno']` for the left hemi and `src[1]['vertno']` for the
> right.
>
> Parcellations are generally defined (by FreeSurfer) on the entire high
> resolution cortical surface, and thus should contain many more points than
> our decimated source space.
>
> So, for a given source space (e.g. ico 4, 2562 sources per hemisphere) I
>> would expect to find the vertices 0...2561 in the parcellation.
>>
>
> The parcellation can have holes. In the case of "aparc" the medial wall
> vertices are missing:
>
> >>> import surfer
> >>> brain = surfer.Brain('fsaverage', 'lh', 'white', views='med')
> >>> brain.add_annotation('aparc', borders=False)
>
> [image: Screenshot from 2019-09-06 09-58-16.png]
>
> Also keep in mind that the decimated source space vertices being numbered
> 0 to 2561 is a property unique to `fsaverage` (and how its spherical mesh
> is arranged), in general for other subjects these can and will be integers
> spanning the whole ~100k brain space.
>
> Eric
>
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