Hi - this could be due to a number of different issues. I wouldn't
normally expect flipping Z (vertically) to make any difference to the
BET output.
The one thing I would try would be to set the -c option (brain
centre) by hand to test if that helps things. If not, feel free to
send us the data to have a quick look at:
Please upload the files in a single compressed tarfile to
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
and then email me the upload ID.
Cheers, Steve.
On 7 Jun 2007, at 10:23, Ed Gronenschild wrote:
> Hi,
>
> Using BET (v1.2) on axial (transversal) T2 stacks I get very bad
> results: only part of
> the brain is extracted. Using different settings with the -f and -g
> options does not
> produce much better results (btw, no other options were used).
> Therefore, a few questions arise:
>
> 1.
> The stacks measures 512 * 512 pixels with 24 slices.The voxel size is
> 0.4492 * 0.4492 * 5.0 mm.
> The fact that the voxels are not cubic could that be a problem?
>
> 2.
> If I inverse Y (flip the stack vertically) the results become even
> worse.
> Is BET sensitive to spatial orientation of the stack?
>
> Ed Gronenschild, PhD
> Maastricht University
> Dept. of Medical Informatics
> Maastricht, The Netherlands
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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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