Hallo,
I might have found a workaround for our problem. Just in case anybody
else is experiencing the same problems. We just lowered
the intensity of the 5% highest values in the 3D-datasets to the 95%
cap. Now the segmentation looks good though I'm still
not sure why it went wrong in the first place. If anybody has an idea......
Cheers,
Wolfgang
Wolfgang Weber-Fahr schrieb:
> 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
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