s_fe_fit_predator.m

function fe = s_fe_fit_predator(bval,tractographyType)
%
% This function:
%  - Initializes a LIFE structure from a candidate connectome
%  - Generates an optimized connectome from a cadidate connectome using 
%  LIFE method
%
%  fe = s_fe_fit()
% 
% INPUTS:  none
% OUTPUTS: fe structure the optimized life structure
%
% Copyright Franco Pestilli (2013) Vistasoft Stanford University

if notDefined('recompute'), recompute=false; end % is true will recumpute the file and overwrite it

% Get the base directory for the data
if ~isempty(bval)
    datapath = '/marcovaldo/frk/2t2/predator/';
    subjects = {'FP_150dirs_b1000_2000_4000_2iso'};
else
    datapath = '/marcovaldo/frk/2t1/predator/';
    subjects = {...
        %'FP_96dirs_b2000_1p5iso', ...
        %'MP_96dirs_b2000_1p5iso', ...
        %'HT_96dirs_b2000_1p5iso', ...
        %'KW_96dirs_b2000_1p5iso', ...
        'JW_96dirs_b2000_1p5iso', ...
        %'KK_96dirs_b2000_1p5iso', ...
        };
end

if notDefined('tractographyType'), tractographyType = 'tensor';end

for isbj = 1:length(subjects)
    % Build the file names for the diffusion data, the anatomical MR, the fiber
    % group containing the connectome and the
    dwiPath  = fullfile(datapath,subjects{isbj},'diffusion_data');
    if ~isempty(bval)
        dwiFiles = dir(fullfile(dwiPath,sprintf('*%s*.gz',num2str(bval))));
    else
        dwiFiles = dir(fullfile(dwiPath,sprintf('run*.gz')));
    end
    dwiFile       = fullfile(dwiPath,dwiFiles(1).name);
    dwiFileRepeat = fullfile(dwiPath,dwiFiles(2).name);
    t1File        = fullfile(datapath,subjects{isbj},'anatomy','t1.nii.gz');
    
    % Directory where to save the fe structures
    savedir       = fullfile(datapath,subjects{isbj},'connectomes');
    
    % Now find all the fiber files that we will analyze
    fibersPath    = fullfile(datapath,subjects{isbj},'fibers');
    if ~isempty(bval)
        fgFiles       = dir(fullfile(fibersPath,sprintf('*%s*%s*.pdb',num2str(bval),tractographyType)));
    else
        fgFiles       = dir(fullfile(fibersPath,sprintf('*.pdb',tractographyType)));
    end
    % We build one modelper fiber group, whole brain fiber group
    for iFib = 1:length(fgFiles)
        
        % The final connectome and dat astructure will be saved with this name:
        [~,feFileName] = fileparts(fgFiles(iFib).name);
        feFileName = [feFileName,'_recomputed'];
        
        % Buil a full-file of the fibers and the FE structure
        fgFileName = fullfile(fibersPath,fgFiles(iFib).name);
        feTempPath = fullfile(savedir,feFileName);
        
        if ~(exist([feTempPath,'.mat'],'file') == 2) && ~recompute
            % Intialize a local matlab cluster if the parallel toolbox is available.
            feOpenLocalCluster;
            
            % Initialize the Connectome
            fe = feConnectomeInit(dwiFile,fgFileName,feFileName,savedir,dwiFileRepeat,t1File);
            %feConnectomeSave(fe);
            
            M    = feGet(fe,'mfiber');
            dSig = feGet(fe,'dsigdemeaned');
            %clear fe
            
            % Fit the model and cull. This will take some time...
            fit = feFitModel(M,dSig,'bbnnls');
            %clear M dSig
            
            % Reload the Fe structure, add the fit and save it back to disk
            %disp('Re-loading the Fe structure to save the fit...')
            %load([feTempPath,'.mat'])
            
            fe = feSet(fe,'fit',fit);
            clear fit
            
            % Save it
            feConnectomeSave(fe);
            
            % Close the matlab pool, this will limit the amount of memory build up
            matlabpool close
        else
            disp('Found FE file not re-computing...')
        end
    end
end

% Exit matlab
exit

return