Hallo,
thanks a lot for the answer. We tried different parameters for the FAST
bias field correction, but the segmentation - especially the seperation
between grey matter and white matter - just was not very good. When
using the SPM bias field correction prior the segmentation, the FAST
segmentation looked quite promising, only that some of the brightest
spots (GM) are clasified as CSF.... .I wonder about the algorithm which
puts some of the brightest voxels into the group with the lowest mean
value. I could attach or upload a little pdf (70kB) showing the problem.
Thanks for any help.
Wolfgang
Steve Smith schrieb:
> 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
>>
>
>
> ---------------------------------------------------------------------------
>
> 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
> ---------------------------------------------------------------------------
>
>
--
----------------------------------------------------------
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
|