Hi - have you tried the full range of BET options (you can just run
BET on its own for now, to get that sorted before running all of
SIENA). For example, the -B BET option?
Cheers.
On 21 Aug 2009, at 00:49, S. Hsieh wrote:
> Hi there,
>
> I would like to use SIENA to estimate volume loss with two scans
> taken of
> the same patient.
>
> There exists already at Time 1 a significant amount of brain atrophy
> which
> may be the reason for some of the difficulty that I am having.
>
> When SIENA uses BET, it misses some portions of the brain, while
> taking in
> the orbits and the neck. I have tried to change the fractional
> intensity
> values (using values <0.5) but this has not helped. Are there other
> options
> that I should use in the command line in SIENA?
>
> Alternatively, should I try to remove non-brain tissue manually from
> each
> image and then submit only brain tissue into SIENA?
>
> Thanks in advance!
>
> S. Hsieh
>
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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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