Hi,
I've uploaded a zip-file rat_segment.zip (4MB) with the reference
Number 650137.
It contains:
original.nii - The brain image before bias correction
spm_debias.nii - After spm debias
debias_seg.nii - The semgmented file from spm_debias.nii
containing my problem in the dentate gyrus
result.pdf - A one page spm check-reg output
documenting my problem.
Thanks amd Cheers. I really appreciate any help or hint.
Wolfgang
Mark Jenkinson wrote:
> 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
>>
>
--
----------------------------------------------------------
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
