afni.nimh.nih.gov

Since I don't know how to duplicate this problem (it works OK on our cluster), I can only make a suggestion.

Try doing this sequence (csh syntax)

Xvfb :88 -screen 0 1024x768x24 >& /dev/null &
setenv DISPLAY :88
3dSkullStrip {whatever}
unsetenv DISPLAY
killall Xvfb

Here, you are starting a virtual (hidden) X11 server, called Xvfb, and telling other programs that follow it to use that.

Maybe that will work??