Hi Ziad & Rick,
thank you for your quick responses.
To clarify: the error message I posted above is the result of running 3dSkullStrip -input x -prefix y -visual
When I ran SUMA and Afni with -niml option, the programme seemed to process but eventually stopped and crashed - there was no evidence of any progress based on the log or on the visualisation of the axial.
I have found the threads regarding Ubuntu, which is why I am attempting to recompile SUMA - this is working ok so far though the Afni/SUMA programmes are still not running properly. If there is no easy fix you know of re Ubuntu I\'ll have to keep trying.
Thanks.
Sarah