Hi - yes, this is still related to the NEUROLOGICAL convention you are
using in these Brainweb-derived files, which is a problem for FAST and
many other NIFTI-reading programs at this point. If you run:
fslswapdim t1_pn3_rf20_ns -x y z fixed
fslorient -swaporient fixed
fast -e -ov -os fixed
You get a very nice segmentation. Otherwise the FAST output is L-R
swapped relative to the input, which would explain your poor overlap
measures.
Cheers.
On 6 Dec 2007, at 16:24, On Tsang wrote:
> for archival purposes:
>
> Dear Steve,
>
> Thank you for your offer to help. The file I am attaching is the skull
> stripped Brainweb T1-w phantom and I just used the default FAST
> settings by
> calling 'fast filename.nii'. From the output image, I extract the
> different
> tissue classes. Thank you again for your time.
>
> Best,
> On Tsang
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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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