afni.nimh.nih.gov

One problem we have seen with El Capitan, 10.11 is with dual monitors and putting the menu on the secondary monitor on the right. That seems to result in afni disappearing into some sort of space limbo / twilight zone. The only way we found to avoid this to make sure the menu bar and dock remain on the primary monitor. Apple's Display preferences allows dragging the menu bar from one monitor to another. Try that and see if it works for you.