Hi. BET is not sensitive to axis direction except that the -g option only
applies a gradient to the -f threshold in the "z" direction. The easiest
fix to changing this direction is to first re-orient the images using
avwswapdim.
Thanks, Steve.
On Mon, 13 Oct 2003, Philipp S[ISO-8859-1] ämann wrote:
> Dear FSL users,
> dear Steve,
>
> we have a problem with the BET function used for sagittal (124 slices) gapless T1-
> weighted volumes. While tuning the parameters f and also g we realized that the g-
> gradient would not be applied in the top-down-direction (superior-inferior
> anatomically) of our images (analzye-format), but from left to right.
>
> With f around 0.25 and g=0 and some shifting of the centre of the starting mesh
> results were reasonable in the cortical area, but still problematic in the basal area
> (skull base and orbital area).
>
> Now the question came up if BET is sensitive to the orientation of the images and if
> therefore the images should be rotated before BET.
>
> Do you have any recommendations for us?
>
> Thanks very much for your help,
>
> Philipp Sämann
> NMR Study Group
> Max-Planck-Institute of Psychiatry. 80804 Munich
> tel. 0049-89-30622-413
>
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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