vsoch/print_dr_report.m

## print_dr_report.m
function print_dr_report(imgfolder)
% This function takes a folder of images produced by visual_dr
% and prints and html report page

filey = fopen([imgfolder 'index.html' ],'w');

% Print top of html file
fprintf(filey,'%s\n','<html><body><h2>Dual Regression Report</h2>');

% Get all images in folder
images = dir([ imgfolder '*.png' ]);
for i=1:length(images)
    img = images(i).name;
    fprintf(filey,'%s\n',[ '<img src="' img '" \>' ]);
end
fprintf('%s\n','</body></html>');
fclose(filey);

## visual_dr.m
function visual_dr(DRdir,bgimg)
% This function will create a web report to visualize dual regression
% results.  The figures print exactly the size of the open figure 1,
% so you might want to open and size it to your liking before running
% the script.

% INPUT
% bgimg is the background image (must be same size as dr output)
% DRdir is the dual regression directory

% OUTPUT
% Will be web report in the dual regression directory
%
% REQUIREMENTS - imoverlay:
% http://www.mathworks.com/matlabcentral/fileexchange/10502-image-overlay

% Read in the background image
bg = spm_read_vols(spm_vol(bgimg));
bgnorm = zeros(size(bg));

% Set output image directory
outdir = [DRdir '/report/' ];
mkdir(outdir);

for b=1:size(bg,1)
    bgnorm(b,:,:) = (bg(b,:,:) - mean(bg(:))) / std(bg(:));
end

% Convert to between 0 and 1
bgnorm = (bgnorm - min(bgnorm(:))) ./ (max(bgnorm(:) - min(bgnorm(:))));

% Read in the number of contrasts and names
filey = fopen([ DRdir '/design.con' ],'r');
contrasts = textscan(filey,'%s','delimiter','\n');

numCons = 0;
for c=1:length(contrasts{1})
    if regexp(contrasts{1}{c},'/ContrastName*') == 1
        numCons = numCons + 1;
        conNameIdx = regexp(contrasts{1}{c},'"*"');
        cons{numCons} = contrasts{1}{c}(conNameIdx(1)+1:conNameIdx(2)-1);
    end
end

% Get the number of corrected p contrast files
files = dir([ DRdir '/dr_stage3_ic00*_tfce_corrp_tstat1.nii.gz']);

% For each thresholded map, display and slice on the background image, for
% each contrast
for m=1:length(files)

    for c=1:length(cons)
        fig = figure(1);
        % Unzip and read in the component/contrast image
        mrname = regexprep(files(m).name,'tstat1',['tstat' num2str(c) ]);
        corrmap = gunzip([ DRdir '/' mrname ]);
        corrmap = spm_read_vols(spm_vol([ corrmap{1} ]));

        % Get the cluster center of the activation
        xyz = regionprops(uint8(corrmap), 'Centroid');

        if ~isempty(xyz)
            if length(xyz.Centroid) == 3
                xyz = floor(xyz.Centroid);

                % for each xyz dimension
                color = rand(3,1);
                subplot(1,3,1); % z
                disp = imoverlay(rot90(bgnorm(:,:,xyz(3))),rot90(corrmap(:,:,xyz(3))),color);
                imagesc(disp); axis off;
                title([ 'Comp #' num2str(m) ' Contrast: ' cons{c}]);
                subplot(1,3,2); % x
                disp = imoverlay(rot90(squeeze(bgnorm(xyz(1),:,:))),rot90(squeeze(corrmap(xyz(1),:,:))),color);
                imagesc(disp); axis off
                subplot(1,3,3); % y
                disp = imoverlay(rot90(squeeze(bgnorm(:,xyz(2),:))),rot90(squeeze(corrmap(:,xyz(2),:))),color);
                imagesc(disp); axis off

                set(gcf, 'PaperPositionMode','auto')
                saveas(fig,[outdir 'comp' num2str(m) '_tstat' num2str(c) '.png' ])
            end
        end
    end
end

print_dr_report(outdir);

end
	function print_dr_report(imgfolder)
	% This function takes a folder of images produced by visual_dr
	% and prints and html report page

	filey = fopen([imgfolder 'index.html' ],'w');

	% Print top of html file
	fprintf(filey,'%s\n','<html><body><h2>Dual Regression Report</h2>');

	% Get all images in folder
	images = dir([ imgfolder '*.png' ]);
	for i=1:length(images)
	img = images(i).name;
	fprintf(filey,'%s\n',[ '<img src="' img '" \>' ]);
	end
	fprintf('%s\n','</body></html>');
	fclose(filey);
	function visual_dr(DRdir,bgimg)
	% This function will create a web report to visualize dual regression
	% results. The figures print exactly the size of the open figure 1,
	% so you might want to open and size it to your liking before running
	% the script.

	% INPUT
	% bgimg is the background image (must be same size as dr output)
	% DRdir is the dual regression directory

	% OUTPUT
	% Will be web report in the dual regression directory
	%
	% REQUIREMENTS - imoverlay:
	% http://www.mathworks.com/matlabcentral/fileexchange/10502-image-overlay

	% Read in the background image
	bg = spm_read_vols(spm_vol(bgimg));
	bgnorm = zeros(size(bg));

	% Set output image directory
	outdir = [DRdir '/report/' ];
	mkdir(outdir);

	for b=1:size(bg,1)
	bgnorm(b,:,:) = (bg(b,:,:) - mean(bg(:))) / std(bg(:));
	end

	% Convert to between 0 and 1
	bgnorm = (bgnorm - min(bgnorm(:))) ./ (max(bgnorm(:) - min(bgnorm(:))));

	% Read in the number of contrasts and names
	filey = fopen([ DRdir '/design.con' ],'r');
	contrasts = textscan(filey,'%s','delimiter','\n');

	numCons = 0;
	for c=1:length(contrasts{1})
	if regexp(contrasts{1}{c},'/ContrastName*') == 1
	numCons = numCons + 1;
	conNameIdx = regexp(contrasts{1}{c},'"*"');
	cons{numCons} = contrasts{1}{c}(conNameIdx(1)+1:conNameIdx(2)-1);
	end
	end

	% Get the number of corrected p contrast files
	files = dir([ DRdir '/dr_stage3_ic00*_tfce_corrp_tstat1.nii.gz']);

	% For each thresholded map, display and slice on the background image, for
	% each contrast
	for m=1:length(files)

	for c=1:length(cons)
	fig = figure(1);
	% Unzip and read in the component/contrast image
	mrname = regexprep(files(m).name,'tstat1',['tstat' num2str(c) ]);
	corrmap = gunzip([ DRdir '/' mrname ]);
	corrmap = spm_read_vols(spm_vol([ corrmap{1} ]));

	% Get the cluster center of the activation
	xyz = regionprops(uint8(corrmap), 'Centroid');

	if ~isempty(xyz)
	if length(xyz.Centroid) == 3
	xyz = floor(xyz.Centroid);

	% for each xyz dimension
	color = rand(3,1);
	subplot(1,3,1); % z
	disp = imoverlay(rot90(bgnorm(:,:,xyz(3))),rot90(corrmap(:,:,xyz(3))),color);
	imagesc(disp); axis off;
	title([ 'Comp #' num2str(m) ' Contrast: ' cons{c}]);
	subplot(1,3,2); % x
	disp = imoverlay(rot90(squeeze(bgnorm(xyz(1),:,:))),rot90(squeeze(corrmap(xyz(1),:,:))),color);
	imagesc(disp); axis off
	subplot(1,3,3); % y
	disp = imoverlay(rot90(squeeze(bgnorm(:,xyz(2),:))),rot90(squeeze(corrmap(:,xyz(2),:))),color);
	imagesc(disp); axis off

	set(gcf, 'PaperPositionMode','auto')
	saveas(fig,[outdir 'comp' num2str(m) '_tstat' num2str(c) '.png' ])
	end
	end
	end
	end

	print_dr_report(outdir);

	end