Thanks for your prompt reply.
> I suspect that for you the easiest thing
> would be to amend the -S option so that it gave the surface outputs
> you need, and then run the betsurf second-stage stuff separately
I looked at the script, but I don't know how to do that. The -S option
first runs bet2, then applies corrections to the masks with fslmaths calls.
If I add the option to output the surface meshes in the bet2 call, I would
get the same mesh as without the -S option.
Is there a tool I can use to convert a mask to a mesh directly? Or is that
code only in bet2?