Currently if a command line app works with a node in the datamanager it is saved as .nii and passed to the cmdapp, however not every app will necessarily work with .nii.

This could probably be fixed by supporting the file extensions attribute [1] and picking the first one that a writer is available for.

[1] The attribute fileExtensions is allowed for file, image and geometry. fileExtensions can contain a list of comma separated file extensions for optional use by the GUI.
(Taken from the description of the slicer execution model)