Hi,
Yes this is a tricky image to segment - for example,
fast -t2 N00001_brain
gives an ok segmentation if you consider merging two of the output
classes into one CSF class - but there is confusion between CSF and
cortical gray.
As this is such an unusual image I would recommend a more custom
approach. You can choose an intensity threshold by hand and use
avwmaths++ and avwstats++ to estimate CSF volume. I wouldn't
recommend trying to use SiENAX as the ventricles won't match the
standard space masks well.
Cheers, Steve.
On 20 Jun 2007, at 17:37, Flavio Dell'Acqua wrote:
> Hi
>
> I have uploaded data with also an updated snapshot (using also -l
> 10000) ID: 187779
>
> We have tried with -l1000 and -c 2 as suggested. We get an
> improved CSF segmentation but not in the center of ventricles.
> In this area, in the restored data, after bias correction,
> artifactual signal attenuation remains.
>
> Few minutes ago we finished a -l5000 and -c 2 and now we have a
> correct CSF segmentation also in ventricles!
> Vetricles are very huge and looking at these results I think there
> is now a problem with the ventricles
> mask used by sienax/fast...but this is the next step. :-)
>
> just a question: -c 2 is compatible with -r option in
> sienax ? ...we are only interested in CSF and ventricle CSF
> quantification.
>
>
> flavio
>
> Steve Smith ha scritto:
>> Hi - thanks for sending the results snapshot, though really we
>> would need to see the data to get a better idea of what's going on.
>> However, from looking at the snapshot, your ventricles are huge,
>> and the grey-white contrast is very poor, so this may be hard. You
>> may get much better results with just asking for 2-class
>> segmentation (-c 2) and then the bias estimation should work fine
>> anyway hopefully.
>> Cheers, Steve.
>>
>
>
>
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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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