Hi - I would not generally recommend using bias field correction
before running FAST; FAST explicitly models bias field as part of the
processing.
Does that improve things?
Cheers.
On 25 Mar 2009, at 17:41, Wolfgang Weber-Fahr wrote:
> Hallo,
>
> I'm rather new to FSL and try to segment T1-weighted rat brains
> using FAST.
> (3D FISP TE/TR 4/8 ms 0.15*0.12*0.23 mm^3)
>
> After brain extraction (BET), some polishing and bias correction
> (SPM) I used
> fast -t 1 -n 3 -g --nopve ....
> since the contrast is not really good I also tried "-t 3" (PD-
> weighted).
>
> The results are pretty good considering the low contrast, but in
> some parts of
> the images - quite often in the hippocampus (dentate gyrus) - where
> the image intensity is actually highest, areas of
> pixels are strangely misclassified as CSF (lowest intensity).
>
> Can anybody give me a clue about what is going wrong?
>
> Thanks,
>
> Wolfgang
>
>
>
>
>
>
> --
> ----------------------------------------------------------
> Wolfgang Weber-Fahr, Dr.rer.nat.
> Central Institute of Mental Health
> Neuroimaging Department
> J5
> 68072 Mannheim
> Germany
>
> email: [log in to unmask]
> phone: ++49 621 1703 2961
>
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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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