This suggests that ImageJ is doing something reasonable.
What makes you think this (?) ie did you try something that gave unexpected results?
Try this: After you open an MRI,
Plugins > BigDataViewer > Open Current Image, then click and drag your mouse around to change the slicing plane. I hope this will convince you that your data are being treated as a 3d volume (at least by the bigdataviewer plugin).
Not dumb, just new. Keep us posted if you run into something unexpected with particular plugins / algorithms. There are certainly some plugins that work on 2d images only and so won't give you the result you want.