They addressed these concerns in several ways - firstly, yes there is microscopy on corresponding sections demonstrating that fiber-crossings were resolved correctly. Second, DSI imaging was performed on mouse hearts, as myocardium exhibits a strong directional organization but without the crossings shown in brain (negative control).

Unfortunately the full article is paywalled, but the Methods supplement is freely available and discusses these issues.

http://www.sciencemag.org/content/suppl/2012/03/28/335.6076....