Dries - consider using the VideoWriter object. A couple of very basic examples can be found at the given link or at writeVideo, but you should be able to extend them for your purposes. For example,
v = VideoWriter('newfile.avi','Uncompressed AVI');
open(v);
for k=1:10 % assumes 10 images to write to file
writeVideo(v,randi(255,100,200,'uint8'));
end
close(v);
