On Wed, Jan 21, 2009 at 8:44 AM, Steve Smith <[log in to unmask]> wrote:

Ah, good point.  I was thinking more of the options where other programs were run _before_ bet2 as opposed to _after_.

It _might_ be good enough to run bet2 with the mesh output option turned on, using as input the brain-extracted output from the first run of bet with the -S option.   ??

Cheers.



On 20 Jan 2009, at 18:11, Marc Lalancette wrote:

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
afterwards."

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?

Cheers,
Marc Lalancette

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Stephen M. Smith, Professor of Biomedical Engineering
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