[FieldTrip] Defining cfg.neighbourdist at source level

[Robert Oostenveld]

Dear Stephan

In fieldtrip/rpivate/clusterstat around line 194 you can see
      posclusobs = findcluster(reshape(postailobs, [cfg.dim,1]),channeighbstructmat,cfg.minnbchan);
that is the section that should get used (the present code still thinks that source is always a 3d regular grid, which is not the case for a surface grid)

Furthermore, in ft_prepare_neighbours there is the subfunction "compneighbstructfromtri" that is of relevance. 

This is a section of the code that needs to be cleaned up and the clustering along the sheet should become a standard feature instead of something that can be managed by a hack. Concrete code suggestions (evt. through bugzilla.fcdonders.nl) are welcome.

best
Robert




On 31 Jan 2012, at 20:48, smoratti at psi.ucm.es wrote:

> Dear Robert,
> 
> To do clustering on a 3D source surface I always had to "trick" field trip and squeezed the 3D source surface data into a ERF structure treating the 3D surface points as sensors. Then by triangulation I found the neighbors. However, if there is a more elegant method implemented in ft_sourcestatistc, I would be very interested to know how to do it. Where can I find some hints on that?
> 
> Best,
> 
> Stephan
> 
> ________________________________________________________
> Stephan Moratti, PhD
> 
> see also: http://web.me.com/smoratti/
> 
> Universidad Complutense de Madrid
> Facultad de Psicología
> Departamento de Psicología Básica I
> Campus de Somosaguas
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
> 
> and
> 
> Center for Biomedical Technology
> Laboratory for Cognitive and Computational Neuroscience
> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
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> 28223 Pozuelo de Alarcón (Madrid)
> Spain
> 
> 
> email: smoratti at psi.ucm.es
> Tel.:    +34 679219982
> 
> El 31/01/2012, a las 15:37, Robert Oostenveld escribió:
> 
>> Dear Ulrich
>> 
>> If your source locations are defined on a regular 3D grid that can be represented as volume, then the neighbours are trivial to find and you do not have to specify a structure for the neighbours. 
>> 
>> If you have done source reconstruction on a 3D folded cortical sheet that is defined by a triangulated surface, then it is also possible to cluster along the surface. I don't know the details for the cortical sheet clustering from the top of my head, if you are interested please let me know and I'll look them up.  
>> 
>> best
>> Robert
>> 
>> 
>> 
>> 
>> On 30 Jan 2012, at 16:58, Pomper, Ulrich wrote:
>> 
>>> Dear Jörn,
>>> Thanks for you reply. I did mean source-level, so like you said, I am trying to define the neighbouring voxels for each voxel.
>>> As far as I understand, leaving cfg.neighbours blank means that the clustering is done over the time and frequency dimensions only, not over space. 
>>> The FT help reads: 
>>> %If you specify an empty neighbourhood structure, clustering will only be done in frequency and time (if available) and not over neighbouring channels.
>>> 
>>> Has anybody done clustering in source space using all three dimensions and could explain how this works?
>>> Cheers, 
>>> Ulrich
>>> 
>> 
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