Hi.

1. BET should be reasonably robust against bias field effects as the
relevant thresholdings (etc) are computed locally. However if the bias is
really bad you could iterate BET-FAST-BET.

2. Well, there various tweaks possible to BET, though it is already
attempting to get this best segmentation - see the FSL email list archives
for other comments on tuning BET.

Cheers, Steve.



On Tue, 1 Jun 2004, Himachandra Chebrolu wrote:

> Hi Everybody,
>
> SInce this was started ,I wanted to pop in a few questions regarding the bias correction.I've two questions:
>
> 1. Does the bias field correction have any impact on the BET
> algorithm.i.e.if I bias correct the MPRAGE volumes before using BET,does
> that give better performance on the BET.
>
> 2. Is it practically possible to get! a complete brain volume with
> absolutely no non-brain matter automatically?I've been running BET
> volumes but it is picking up considerable amount of non-brain matter
> particularly in the orbital fat region and the tongue etc.
>
> Thanks,
> Himachandra
>
> Clare Mackay <[log in to unmask]>wrote:
> Hi Krish,
>
> I'll be brave and answer this one - since I've asked the same questions
> myself in the past...
>
> 1) As I understand it, the bias field estimations and segmentation
> procedure run iteratively together, so you can't have one without the
> other.
>
> 2) Yes, but you need to output a dilated version of the bias field
> (-oba option) and then run avwmaths_32R (i.e. need to have floating
> point data). You can revert back to more sensibly sized bit depths after
> you've multiplied by the bias field
>
> so:
>> fast -l 100 -i 8 -oba 100
> avwmaths_32R [input] _abias
>
> Cheers,
> Clare
>
> ___________________________________________________
> Clare E. Mackay, Ph.D.
> Research Fellow,
> Prince of Wales International Research Centre (POWIC),
> University Department of Psychiatry,
> Warneford Hospital, Oxford. OX3 7JX. UK
>
> tel: 01865 455910 fax: 01865 455922
> OCMR: 01865 221866 / 72
> [log in to unmask] www.psychiatry.ox.ac.uk/powic
> ___________________________________________________
>
> >>> [log in to unmask] 01-06-2004 13:00:59 >>>
> Hi,
>
> We have just started generating mp-rage volume scans from our new 3T
> Siemens
> Trio, using the 8-channel head coil.
>
> The images look great, with excellent grey-white matter contrast, but
> there
> is a noticeable bias field.
>
> Fast! seems to make a great job of bias-correcting these images, but I
> have
> two questions:
>
> 1) I wonder whether it is possible (on the command line) to simply
> bias-correct the images, without doing the segmentation? Or does the
> segmentation not really contribute to the processing time?
>
> 2) Is it possible to apply the generated bias field image to another
> image
> (i.e. The non-skullstripped image)? Is it simply a matter of
> multiplying in
> avwmaths?
>
> Thanks and all the best,
>
> Krish
>
> --
> Dr K.D. Singh
> Senior Lecturer and Convenor of the Neuroimaging Research Group,
> Director, MRI Research Centre,
> Neurosciences Research Institute
> Aston University, Birmingham B4 7ET, U.K.
> Tel/Fax: +44 (0)121 [359 3611 ext 5176/5190]/[333 4220]
> [log in to unmask], http://www.aston.ac.uk/lhs/staff/singhkd/
>
> ---------------------------------
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Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator

Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)

[log in to unmask] http://www.fmrib.ox.ac.uk/~steve