vof_lateralmedial_life.m

function vof_lateralmedial_life(feFileToLoad, fibername, roisDir, roiNames, roiOperations, nboots, nmontecarlo)

% This function computes the strength of evidence for lateral and medial
% VOF. LIFE code and MBA code by Franco Pestilli are required.
% https://github.com/francopestilli/life
% https://github.com/francopestilli/mba
%
% INPUT:
% feFileToLoad: a full path to .mat file containing fe structure (generated by LIFE code). Use strings for loading multiple connectome data.
% fibername: a name for fibers. Used for output file name.
% roisDir: a directory containing waypoint ROI mat files
% roiNames: names for waypoint ROIs (string)
% roiOperations: 'and', selecting fiber passing through the ROI, 'not',
%                 excluding fiber passing through the ROIs, 'endpoints', selecting fibers
%                 with endpoint within the ROI.
% nboots: number of bootstrap. Default is 100000.
% nmontecarlo: number of the repetition of montecarlo simulation. Default is 5.
%
% In the paper, HT used the VOFPlane2 as 'AND' ROIs. Lateral/Medial white
% matter ROIs (with respect to CoS) were used as either 'endpoints' or
% 'not' ROIs.
%
% EXAMPLE:
% feFileToLoad{1} = '/home/vof/data/S1/life/LH_1stconnectome_fe.mat';
% feFileToLoad{2} = '/home/vof/data/S1/life/LH_2ndconnectome_fe.mat';
% feFileToLoad{3} = '/home/vof/data/S1/life/LH_3rdconnectome_fe.mat';
% fibername = 'LVOF_MedialFromCoS';
% roisDir = '/home/vof/data/S1/ROIs/Waypoint/';
% roiNames = {'LH_VOFPlane2.mat','LH_LateralFromCoS_WM.mat','LH_MedialfromCoS_WM.mat'};
% roiOperations = {'and','not','endpoints'};
% vof_lateralmedial_life(feFileToLoad, fibername, roisDir, roiNames, roiOperations);
%
% Copyright (c) Hiromasa Takemura and Franco Pestilli, 2013, Stanford VISTA team

% Argument checking
if notDefined('nboots')
    nboots = 100000;
end
if notDefined('nmontecarlo')
    nmontecarlo = 5;
end

% Define file name for output .mat file
savematfile = [fibername, '_StrengthEvidence.mat'];

sizecon = size(feFileToLoad);

for connum = 1:sizecon(2)
    
    % Read ROI files
    for iroi = 1:length(roiNames)
        rois{iroi} = fullfile(roisDir,roiNames{iroi});
    end
    
    % Load LIFE file
    disp('loading the LiFE structure...')
    if ischar(feFileToLoad{connum})
        fprintf('Loading %s ...\n',feFileToLoad{connum})
        load(feFileToLoad{connum});
    else
        fe  =feFileToLoad{connum};
        clear feFileToLoad;
    end
    
    % Extract the fiber group from the FE structure
    fg = feGet(fe,'fibers acpc');
    
    % Segmenting VOF from connectome
    fprintf('Segmenting the Tract from Connectome ...\n')
    [fgsegment, keepFascicles] = feSegmentFascicleFromConnectome(fg, rois, roiOperations, 'prob connectome');
    
    % Exclude outliers
    fprintf('Excluding outliers from Fasciculus ...\n')
    [fgsegment2 keepFascicles2] = vof_gradient_removeoutlier(fe, keepFascicles,2,rois{1},rois{2});
    [fgsegment3, keepFascicle3] = mbaComputeFibersOutliers(fgsegment2,3,3,25);
    keepFascicles4 = keepFascicles2;
    keepFascicle2matrix = find(keepFascicles2);
    
    for kj = 1:length(keepFascicle3)
        if keepFascicle3(kj)==0,
            keepFascicles4(keepFascicle2matrix(kj)) = 0;
        else
        end
    end
        
    % Start to test the tract
    fprintf('Testing the Tract ...\n')
    [se{connum}] = feVirtualLesion(fe, keepFascicles4);
    
    
end
% save file
save(savematfile, 'se');

end