et_concatenateconnectomes.m

function et_concatenateconnectomes(fginput,fname, numconcatenate)

% Concatenate connectomes generated by different parameters and algorithms
% to create new candidate set of connectomes. 
% 
% In Ensemble Tractography, this function will be used to create a new
% candidate Ensemble Tractography Connectome (ETC). The candidate ETC
% should be futher optimized using LiFE. 
%
% In this function, we simply concatenate streamlines in each connectome
% (fg structure) to create new connectome as fg file. 
%
% The default in this function is including all streamlines to output new connectome files 
% (add-them-all). 
% 
% If you specify the parameter "numconcatenate", you could include a subset
% of streamlines from each connectomes
%
% Reference:
% Takemura, H., Caiafa, C., Wandell, B.A. & Pestilli, F. (under review) Ensemble
% Tractography. 
% 
% INPUT:
% fginput: Files of connectomes generated by various type of tractography
%          algorithms and parameters (.pdb or .mat format)
% fname: File name for output file. (.pdb or .mat format)
% numconcatenate: This variable defines how many streamlines from each
%                 connectome shold be included into ETC-rand candidate connectomes. 
%                 1 x N matrix.
%
% (C) Hiromasa Takemura, CiNet HHS/Stanford VISTA Lab 2015
% 
%
% EXAMPLE:
% fginput = {'S1_LH_Occipital_curv0p25SPC_cand.mat',
% 'S1_LH_Occipital_curv0p5SPC_cand.mat',
% 'S1_LH_Occipital_curv1SPC_cand.mat',
% 'S1_LH_Occipital_curv2SPC_cand.mat'}
%  numconcatenate = [40000 40000 40000 40000];
% fname = 'S1_LH_Occipital_ETCrand_cand.mat';
% et_concatenateconnectomes(fginput, fname, numconcatenate) 

% Load fgfile to input;
for i = 1:length(fginput)
   fg{i} = fgRead(fginput{i});   
end

% Unless specified, add all streamlines into new connectomes.
if notDefined('numconcatenate'), 
   for k=1:length(fginput)
   numconcatenate(k) = length(fg{k}.fibers);
   end
else
    
% Argument checking
if ~length(fginput) == length(numconcatenate)
 error('Matrix size of fginput and numnconcatenate should be identical.');
end    
end

% Create fg structure
fg_etc = fgCreate;

% Set name for connectome file to save
fg_etc.name = fname;

% Concatenate connectomes
for i = 1:length(fginput)
    if i == 1
       fg_etc.fibers(1:numconcatenate(i)) = fg{1}.fibers(1:numconcatenate(1));       
    else
       fg_etc.fibers(1+sum(numconcatenate(1:(i-1))):sum(numconcatenate(1:i))) = fg{i}.fibers(1:numconcatenate(i));       
        
    end
end

% Transpose dimension of fiber matrix
fg_etc.fibers = transpose(fg_etc.fibers);

% Write file
fgWrite(fg_etc);