Hi,
One problem with the bet wrapper script ("bet") is that the range of
possible options and combinations of options that people might want is
huge, and it's therefore very hard to script this so that all
combinations would work together in all cases. Hence the best thing
for you if you want the surface stuff as well as the -S options would
be to take a local copy of the bet script and customise it to give you
the combination you want. 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I guess the FAQ is out of date - Matthew, could you update it please?
Cheers, Steve.
On 19 Jan 2009, at 19:01, Marc Lalancette wrote:
> Hello,
>
> I started playing with bet last week, trying to get a good inner
> skull mesh,
> with limited success. I have a few comments/questions.
>
> 0. Well just a quick comment, but wouldn't it be MUCH better to have
> a real
> forum instead of a mailing list? As a new user with a simple
> question I
> don't care to receive all the forum content by email, and a forum
> usually
> allows one to subscribe to new posts by email for those who really
> want to.
> Anyway, on to my real questions.
>
> 1. I wanted to try bet with the -S option to remove eye blobs from
> the brain
> mask, but apparently, -S excludes the -e option (no mesh was
> outputted) so I
> can't use betsurf with the better mask that -S provides. Long term:
> can
> this be fixed? Short term: Anything else I can do to get the brain
> mesh
> from the -S brain mask?
>
> 2. In the command line help, -c says "voxels not mm", but the online
> faq
> says the opposite (mm not voxels). I think the command line is
> right, is
> this the case? (Also, obviously, the wrong one should be corrected.)
>
> Cheers,
> Marc Lalancette,
> Toronto Hospital for Sick Children
>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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