[FieldTrip] extracting a continuous patch on a mesh

[parham hashemzadeh]

Hi All
  Is there a Matlab implementation of openMEEG lying around somewhere?
  I was wondering, if openMEEG has a pure Matlab or python 
implementation.
  Pure form.
  Many of us (INCLUDING ME) are using code, without really digging deep 
into the details.
  I would be grateful, if it can be shared.
  Many thanks
best regards parham

On 2018-04-23 13:15, Maximilien Chaumon wrote:
> Hi all,
> 
> So I coded something that could perhaps be useful to others. It grows
> a patch around a seed up to a certain distance. See below
> 
> function [list] = mesh_patch(mesh,seed,dmax)
> 
> % [list] = mesh_patch(mesh,seed,d)
> %
> % return the list of connected vertices that are at most d mesh.unit
> away
> % from seed.
> %
> % Maximilien Chaumon 2018
> 
> % measure distance to seed
> seedpos = mesh.pos(seed,:);
> distances = sqrt(sum(bsxfun(@minus,mesh.pos,seedpos).^2,2));
> 
> % crawl starting from seed
> list = crawl(mesh.tri,distances,dmax,seed);
> 
> function final = crawl(tri,d,dmax,vert)
> 
> % bookkeeping: the list of vertices
> persistent listi
> st = dbstack;
> level = sum(strcmp({st.name [1]},'crawl'));
> if level == 1
>     listi = [];
> end
> %
> 
> listi(end+1) = vert; % append this vertex to the list
> 
> conn = tri(any(tri==vert,2),:);% connected vertices
> conn = unique(conn);
> conn(d(conn) > dmax) = []; % remove those that are too far.
> conn(ismember(conn,listi)) = [];%keep only vertices that have not been
> crawled yet
> for i = 1:numel(conn)
>     crawl(tri,d,dmax,conn(i));% move to next
> end
> 
> % bookkeeping: return the list at last
> if level == 1
>     final = listi; % return list if it's last call
> end
> 
> Le ven. 13 avr. 2018 à 16:16, Maximilien Chaumon
> <maximilien.chaumon at gmail.com> a écrit :
> 
>> Dear all,
>> 
>> I'm trying to extract a connected patch of vertices at most say 2 cm
>> away from a given seed.
>> Is there an easy way to do this in FieldTrip?
>> 
>> Many thanks,
>> Max
> 
> 
> Links:
> ------
> [1] http://st.name
> 
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-- 
best regards
Parham Hashemzadeh
Research Associate
Department of Applied Mathematics and Theoretical Physics
University of Cambridge, UK.
email: hashemzadeh at damtp.cam.ac.uk