1. For extra bet options sucj as -g the easy thing to do is to edit the
fsl/bin/siena script (or make a local copy) and find the _two_ calls to
bet and insert the option you want.

2. If you are still worried about dodgy tissue left in (which in siena
will probably have very little impact on the final values, particularly
when compared with the other various sources of "noise" in the whole
imaging and measurement process - see the paper) then you can check the
effect by manually editing and then re-running siena with the bet commands
commented out.

Cheers - hope this helps!

On Mon, 12 Jul 2004, Isabell Wartenburger wrote:

> dear fsl-experts,
> i would like to use siena on a large number of subjects (all will be
> scanned 2-3 times). after i have tried almost all options, the bet
> brain extraction is still NOT ok around the eyeballs. a combination of
> the [-f 0.3] and [-g -0.1] gets it close, but the extracted brain is still not
> perfect, some of the eyeballs and brainstem is detected as brain.
> is there a siena script there the [-g]-option is included?
> or would you advise me to manually remove (i.e. paint out) the critical
> areas (i.e. the eyeballs) in the original data?
> thank you very much for your help!
> best regards, isa.
> - - -
> Dr. Isabell Wartenburger
> Berlin NeuroImaging Center, Dept. of Neurology
> Charité Campus Mitte, Schumannstr. 20/21
> 10117 Berlin, Germany
> Phone:  ++49-30-450 560 194
> Fax:    ++49-30-450 560 952
> - - -

 Stephen M. Smith  DPhil
 Associate Director, FMRIB and Analysis Research Coordinator

 Oxford University Centre for Functional MRI of the Brain
 John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
 +44 (0) 1865 222726  (fax 222717)

 [log in to unmask]