When I load .nii volumes using the "Add Data" dialog, The filename shows up normally in the dialog. I could change it here if I wanted to, to be something different. For example, I select the file called "myimage.nii", and there is a text box that is pre-filled with "myimage", which I leave alone. Then, when I click "OK" to load the image, it now shows up in the Data and Volumes modules as "myimage1". In slicer3, this would happen if I tried to load a second copy of an image called the same thing, and I understand that. But it is sometimes confusing when loading images that have names that end in numbers ("subject354" would now be loaded as "subject3541", even the first time I've ever loaded that image).

Could it be that the algorithm that checks if the name is already in use is getting fooled somehow, and it's always adding the "1"? If I try to load the same file again, it seems to correctly iterate to "2".