Hi Rolf,
what happens when you run avwsize and avwhd on this data set? One
possibility is to use the -c option to make sure that bet starts off
inside the brain - this is useful if your data has a lot of neck
included in the image, by default, BET is initialised at the COG
which - if there's a lot of neck - is too low. Another possibility is
to use the -f and -g options, see command line help for more info
cheers
Christian
On 23 Jul 2007, at 17:10, Rolf Heckemann wrote:
> I am getting strange results using bet on a NIFTI file -- it seems to
> use a wrong interpretation of the orientation. For testing, I ran
> "bet file.nii.gz file-bet.nii.gz -g 1": I get an outline that cuts
> into the brain on the right, but leaves the left untouched (expected
> result is a large brain outline at the bottom, small at the top).
> FSLView loads the input file correctly (i.e. S, I, A, P, R and L
> labels are as expected). I tried working around the issue by running
> betpremask on file.nii, but although it generates a reasonably-looking
> premasked image, the same orientation problem occurs when I use bet on
> it.
>
> How can I get bet to read this type of file properly?
>
> Thanks
>
> Rolf
>
>
> --
> Rolf A Heckemann, PhD
> Research Associate
> Division of Neuroscience and Mental Health
> MRC Clinical Sciences Centre
> Imperial College London
> Hammersmith Hospital Campus
> Du Cane Road
> London W12 0HS
> United Kingdom
____
Christian F. Beckmann
University Research Lecturer
Oxford University Centre for Functional MRI of the Brain (FMRIB)
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
[log in to unmask] http://www.fmrib.ox.ac.uk/~beckmann
tel: +44 1865 222551 fax: +44 1865 222717
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