[Master Index] [Index for Toolbox]

# separation

## (Toolbox/separation.m in BrainStorm 2.0 (Alpha))

### Function Synopsis

    [I_pos,I_neg]=separation(v,connectivity_cell)

### Help Text

    SEPARATION - Splitting the brain into 2 parts
     function [I_pos,I_neg]=separation(v,connectivity_cell)

      spliting the brain into 2 parts

      inputs : v : vertices (brain centered), connectivity_cell : result of vertices_connectivity
      outputs : I_pos/I_neg : indices of the vertices corresponding to the positive/negative part of the brain

### Cross-Reference Information

This function is called by

    bem_xfer                           C:\BrainStorm_2001\Toolbox\bem_xfer.m
    c_activ                            C:\BrainStorm_2001\Toolbox\c_activ.m

### Listing of function C:\BrainStorm_2001\Toolbox\separation.m

    function [I_pos,I_neg]=separation(v,connectivity_cell)
    %SEPARATION - Splitting the brain into 2 parts
    % function [I_pos,I_neg]=separation(v,connectivity_cell)
    %
    %  spliting the brain into 2 parts
    %
    %  inputs : v : vertices (brain centered), connectivity_cell : result of vertices_connectivity
    %  outputs : I_pos/I_neg : indices of the vertices corresponding to the positive/negative part of the brain
    %

    %<autobegin> ---------------------- 26-May-2004 11:34:21 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: Visualization
    %
    % At Check-in: $Author: Mosher $  $Revision: 14 $  $Date: 5/26/04 10:02a $
    %
    % This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 24-May-2004
    %
    % Principal Investigators and Developers:
    % ** Richard M. Leahy, PhD, Signal & Image Processing Institute,
    %    University of Southern California, Los Angeles, CA
    % ** John C. Mosher, PhD, Biophysics Group,
    %    Los Alamos National Laboratory, Los Alamos, NM
    % ** Sylvain Baillet, PhD, Cognitive Neuroscience & Brain Imaging Laboratory,
    %    CNRS, Hopital de la Salpetriere, Paris, France
    %
    % See BrainStorm website at http://neuroimage.usc.edu for further information.
    %
    % Copyright (c) 2004 BrainStorm by the University of Southern California
    % This software distributed  under the terms of the GNU General Public License
    % as published by the Free Software Foundation. Further details on the GPL
    % license can be found at http://www.gnu.org/copyleft/gpl.html .
    %
    % FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
    % UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
    % WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
    % MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
    % LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
    %<autoend> ------------------------ 26-May-2004 11:34:21 -----------------------

    % find short and long axes
    larg1=max(max(v(:,1)))-min(min(v(:,1)));
    larg2=max(max(v(:,2)))-min(min(v(:,2)));
    if larg1<larg2
        short_axe=1;
        long_axe=2;
    else
        short_axe=2;
        long_axe=1;
    end
    maxi=max(max(v(:,short_axe)));
    mini=min(min(v(:,short_axe)));

    % test to know whether the cerebellum is included or not
    i_mini=find(v(:,3)==min(min(v(:,3))));
    if v(i_mini,long_axe)<0
        cerebellum=1;
    %     'cerebellum in'
    else
        cerebellum=2;
    %     'cerebellum out'
    end

    % spliting of the brain into 2 parts
    I_maxi=find(v(:,short_axe)==maxi);
    i_maxi=I_maxi(1,1);
    v_vector=i_maxi;
    front=i_maxi;
    stop=0;
    stop_it=zeros(size(v,1),1);
    while stop~=1
        clear stop_it_test;
        stop_it_test=stop_it(front);
        I_az=find(stop_it_test==0);
        clear v_neig;
        clear fronttemp;
        fronttemp=front;
        v_neig=[];
        for i=1:size(I_az)
            v_neig=[v_neig connectivity_cell{front(I_az(i))}];
        end
        v_neigu=unique(v_neig);
        clear v_new_neig;
        v_new_neig=setdiff(v_neigu,v_vector);
        front_nav=[front v_new_neig];
        clear front;
        front=setdiff(front_nav,fronttemp(I_az));
        clear v_test;
        I_iz=find(v(v_new_neig,short_axe)<=0);
        if ~isempty(I_iz)
            if cerebellum==1
                I_z_axe=find(v(v_new_neig(I_iz),3)<4*max(max(v(:,3))));
                if  ~isempty(I_z_axe)
                    I_long_axe=find(v(v_new_neig(I_iz(I_z_axe)),long_axe)<6*max(max(v(:,long_axe))));
                    if ~isempty(I_long_axe)
                        stop_it(v_new_neig(I_iz(I_z_axe(I_long_axe))))=1;
                    end
                end
            elseif cerebellum==2
                I_z_axe=find(v(v_new_neig(I_iz),3)<0.4*max(max(v(:,3))) & v(v_new_neig(I_iz),3)>-0.6*max(max(v(:,3))));
                if  ~isempty(I_z_axe)
                    I_long_axe=find(v(v_new_neig(I_iz(I_z_axe)),long_axe)<0.6*max(max(v(:,long_axe))) & v(v_new_neig(I_iz(I_z_axe)),long_axe)>-0.4*max(max(v(:,long_axe))));
                    if ~isempty(I_long_axe)
                        stop_it(v_new_neig(I_iz(I_z_axe(I_long_axe))))=1;
                    end
                end
            end
        end
        clear I_stop;
        I_stop=find(stop_it==1);
        v_vector=unique([v_vector front]);
        if size(I_stop,1)==size(front,2)
            stop=1;
        end
    end
    I_neg=(setdiff(linspace(1,size(v,1),size(v,1)),v_vector'))';
    I_pos=v_vector';

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