Hi - I'm not sure if you're saying that you'd like to improve the
segmentation output by FAST or the effect of the cortical masking
carried out by affine-transforming a simple cortical standard space
mask onto the data - it sounds like it may be the latter, in which
case you might want to use your own version of $FSLDIR/etc/standard/
avg152T1_strucseg_periph - or it may simply be that your subject is
too different from the MNI152 for a purely affine transformation to
give you a good match of the mask, in which case SIENAX can't help
you there!
Hope this helps - cheers, Steve.
On 21 Oct 2006, at 17:57, Paul Geha wrote:
> Hello,
>
> I am trying to do a cortical volume quantification using Sienax on
> t1 images. When I run it I get
> the output called t1_periph_render. This one shows that there are
> some small areas in the
> fusiform gyrus, and the orbito-frontal cortex. I tried to
> increase the number of iteration with
> the S option (to 15) in Sienax to improve this but this did not
> work. However, if I run FAST on
> the t1 image with the "use a priori probability maps for
> initialising" I get a better peripheral
> gray matter mask in t1_brain_seg1 image with no omissions, but
> this one includes the sub-cortical
> structures and the cerebellum, which I want to exclude.
>
> Can I improve Sienax segmentation in anyway? Please advise.
>
> thanks a lot,
>
> Paul
>
> Paul Geha M.D.
> Northwestern University
> The Feinberg School of Medicine
> Department of Physiology M211
> 303 E. Chicago Ave.
> Chicago, IL 60611
> Tel:312-503 2886
> Fax: 312-503-5101
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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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