[Mne_analysis] filling gaps between a set of concatenated labels

[Martin Luessi]

Hi Denis,

Attached is a script that iteratively grows each label until all the
gaps are filled. It currently only works for a parcellation with small
gaps. You will need to adjust it for your case where you have a large
missing area.

Best,

Martin


On 08/18/14 11:54, Denis-Alexander Engemann wrote:
> The best thing would be to compute a "smooth" enveolope around the
> outermost vertices and just take everything inside. I fear this is not
> as easy to get as it sounds ...
> Anyways, on closer inspection, the actual amount of vertices disjoint by
> th gaps is neglegible. I might not suffer enough to look into it.
> 
> Alex, have we ever thought about adding some set logic to labels? I'm
> thinking of overloading the minus operator for example.
> 
> -D
> 
> On Mon, Aug 18, 2014 at 5:47 PM, Alexandre Gramfort
> <alexandre.gramfort at telecom-paristech.fr
> <mailto:alexandre.gramfort at telecom-paristech.fr>> wrote:
> 
>     hi,
> 
>     you could "smooth" the label (although we should have named it
>     dilate). The current code in stc_to_label could maybe help.
> 
>     HTH
>     Alex
> 
> 
>     On Sat, Aug 16, 2014 at 10:13 PM, Denis-Alexander Engemann
>     <denis.engemann at gmail.com <mailto:denis.engemann at gmail.com>> wrote:
>     > Dear list,
>     >
>     > for a recent analysis I'm assembling a big label (using operator
>     overloading
>     > np.sum(labels)) based on the Brodmann PALS B12 parcelation.
>     > As a result, some gaps remain between adjacent labels.
>     > E.g. see:
>     https://www.dropbox.com/s/rzzzcz1tv1k75si/label_check_lat.png
>     >
>     > I'm wondering about the easisest way to fill these gaps (code-based).
>     >
>     > Best,
>     > Denis
>     >
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-- 
Martin Luessi, Ph.D.

Research Fellow

Department of Radiology
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Harvard Medical School
149 13th Street
Charlestown, MA 02129

Fax: +1 617 726-7422
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