Hi,
Can you please upload your volumetric image to:
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
and send us the reference number?
Hopefully we'll be able to sort it out easily.
All the best,
Mark
On 29 Mar 2009, at 22:37, Wolfgang Weber-Fahr wrote:
> 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
>
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