Thanks Ziad,

here is the error message from 3dSkullStrip:

$ 3dSkullStrip -input MI_anat+orig -prefix anat_test_ns -visual
SUMA_niml_call: Contacting ...
.....Error SUMA_niml_call: WriteCheck timed out (> 2000 ms).
Error SUMA_SendToSuma (SUMA_niml.c:3253):
Failed in SUMA_niml_call
Error 3dSkullStrip (SUMA_3dSkullStrip.c:1631):
Failed to initialize SUMA_SendToSuma

Looks like it could be compatibility with the precompiled SUMA and Ubuntu so trying to recompile SUMA.

In the process of recompiling SUMA there are some problems with opengl dependencies (Ubuntu Feisty), which I am in the progress of working out.

Any suggestions regarding SUMA and Ubuntu? Are there any pre-compiled binaries that work with Ubuntu Feisty?

Thanks for your help
Sarah