I believe that this will be fixed in 3.8 -- I did some bug fixing a few months ago on this, and currently have used the feature without trouble.
I am adding a generic ITK reader to ITK-SNAP 3.8. This should resolve the discrepancy between the GUI and command-line reading. However, I think ITK has to be compiled with MINC support for this to actually work..
Status: open --> wont-fix
Status: open --> wont-fix
Status: open --> wont-fix
Status: open --> wont-fix
Status: open --> wont-fix
Status: open --> wont-fix