You quite probably know which filesystem is short of space. In which case you can use ncdu -x to only count files and directories on the same filesystem as the directory being scanned. – Luke Cousins Jul 21, 2017 at 11:51

best answer. also: sudo ncdu -rx / should give a clean read on biggest dirs/files ONLY on root area drive. (-r = read-only, -x = stay on same filesystem (meaning: do not traverse other filesystem mounts) ) – B. Shea Sep 21, 2017 at 15:52

I personally would use something like this: sudo ncdu --confirm-delete -rx / --exclude /mnt. This allows you to push d on files to delete them. It also won’t scan any files that you have in /mnt.