Have you tried the -B option to bet? You can pass that into SIENA by
adding onto the end of the SIENA command
-B "-B"
Cheers.
On 24 Oct 2007, at 20:52, Antonios - Constantine Thanellas wrote:
> Dear fsl users
>
> I want to betpremask (through standard_space_roi) my data in order
> to do
> longitudinal and cross sectional analysis with siena and sienax
> respectively.
>
> Since siena needs the skulls of the original images i can't just do
> a shell
> script that sends as inputs to siena the stripped brain images after
> betpremasking them. I've read in FSL forum that it's better to
> change the
> siena script as follows: "leave BET to extract the skulls, then run
> betpremask and feed, then run again bet on the premasked images and
> feed
> siena with these results." The problem is that siena script is too
> complicated for my scripting skills and i would really appreciate
> if you
> could tell me how to change this script in order to betpremask my
> data first
> (bet_robust totally fails in most of my data which contain big
> protions of
> neck even if i determine the COG with the -c option.That's why i need
> betpremask since it gives me really good results).I use the fsl 4.0
> version
> on ubuntu platform.
>
> How about sienax ? it also needs the skulls in order to register
> the images
> with pairreg? How the sienax script should be changed in order to
> incorporate betpremasking?In this case also, a shell script that
> sends as
> inputs to sienax the betpremasked images wouldn't work..Right?
>
> Thank's a lot for your time
>
> Antonios-Constantine Thanellas
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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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