The check for a running ImageJ instance can block indefinitely.

[odinsbane]

I had a corrupt "/tmp/ImageJ-username-_0-012345.stub" which cause imagej to block indefinitely. The issue happens at line 127 of OtherInstance.java

ImageJInstance instance = (ImageJInstance) new ObjectInputStream(in).readObject();

That method wasn't returning. It's pretty rare, but somewhat obscure when it happens. I had to delete the tmp file and then I could run imagej from the cmd line again.