[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
Search archives:

        External Email - Use Caution        

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



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
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis

Department of Biomedical and Clinical Sciences "Luigi Sacco"
University of Milan
Phone: +39 02 503 19731
via G. B. Grassi 74 - 20157 Milano

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20190913/49fd9da4/attachment-0001.html 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.jpg
Type: image/jpeg
Size: 15760 bytes
Desc: not available
Url : http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20190913/49fd9da4/attachment-0001.jpg 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot from 2019-09-06 09-58-16.png
Type: image/png
Size: 333943 bytes
Desc: not available
Url : http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20190913/49fd9da4/attachment-0001.png 

More information about the Mne_analysis mailing list