Hi - if you run "siena" with the -d option you will get a load of
intermediate images left around such as *_brain_seg.hdr segmentation
output images. Hopefully these will let you find out what you want to
know. It sounds like on these images BET is not giving perfect brain
extraction - you might want to try different BET options by hand and then
put the optimal setting into siena with the -f option.
Cheers, Steve.
On Sun, 9 Nov 2003, Philipp S[ISO-8859-1] ämann wrote:
> Dear FSL users,
> dear Steve
>
> we are using SIENA for atropy estimation on T2- and T1-weighted images with some
> manual correction of the BET masks, and all in all it is working out fine.
>
> However, the some result (render) images with the color coded edge-point motion
> show areas outside the brain (esp. sinus, orbitae etc.), probably caused by irrelevant
> borderlines through imperfects masking. Is there a possibility to check an
> intermediate image with edge points shown for each single image (not the flowneg-
> image with the processed edge motion)? An image of the kind we are thinking of is
> shown in the FMRIB Technical report on SIENA, page 7.
>
> Thanks very much,
> Philipp Sämann
>
> Max-Planck-Institute of Psychiatry, Munich
> NMR Research Group
> Head: PD Dr D. Auer
>
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] http://www.fmrib.ox.ac.uk/~steve
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