There is a simple but very inconvenient bug when running BIS functions from the console in Windows (does not happen in the Linux version). It was found in the functions bis_linearintensityregister and bis_nonlinearintensityregister - I don't know about other functions. 

When calling the functions with a Nifti file as input, an error is generated: 

"Error -- Failed to Load Image as DICOM" 

It appears that the function does not recognize that the file format is Nifti - however when opening the associated GUI and loading the file manually, the format is correctly recognized (or when running the console command in Linux). 

This is frustrating because it forces me to replace an otherwise streamlined procedure with either a manual step using the GUI, or with using a Linux virtual machine just for this step (or try using SPM for this purpose).