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vsoch/print_dr_report.m

Last active December 21, 2015 14:59
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visual_dr creates and prints a web report for a dual regression run with FSL. 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. visual_dr is the main script to run, and it uses print_dr_report to create a web report, and imoverlay to overlay maps on the backgr…
Raw
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);
Raw
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
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