Hi,
The bias correction is interleaved with segmentation,
even in the initial stages, so with a poor initial segmentation
from a non-betted brain it probably won't work.
If the bias field is very strong then you can get a
reasonable estimate of the bias field just by smoothing
the image a lot. We sometimes use this to deal with
strong surface-coil bias fields.
All the best,
Mark
Matt Glasser wrote:
> If you used only the bias correct function of FAST, would it be possible to
> improve the brain extraction of files with bias?
>
> Thanks,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Steve Smith
> Sent: Friday, February 13, 2009 3:35 AM
> To: [log in to unmask]
> Subject: Re: [FSL] FAST without BET
>
> Hi, no this isn't generally possible, primarily because the histogram
> is so messy if you don't pre-BET that the mixture modelling in FAST
> doesn't work well.
> Cheers.
>
>
> On 13 Feb 2009, at 09:21, Lucas Eggert wrote:
>
>
>> Dear Experts,
>>
>> is it possible to segment a T1 image into its three main tissue
>> tpyes (GM, WM, CSF) with FAST, without using BET as a preprocessing
>> step, and still get feasible results?
>>
>> I would like to compare different preprocessing steps and their
>> influence on the segmentation result. For this purpose I need to
>> apply FAST to T1 images that are not preprocessed at all, or not
>> preprocessed with BET.
>>
>> I tried it FAST without BET once on a sample data set, but the
>> resulting p-maps for GM were unusable.
>>
>> Any help would be very much appreciated.
>>
>> Best regards,
>> -Lucas
>>
>>
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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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