Hi,
On 24 Jan 2008, at 21:57, Jeff Spielberg wrote:
> Hi, I have a couple of questions regarding Fsl-vbm and First. The
> scans we
> have been using for both have some signal loss superiorly and
> inferiorly.
> Due to this we do not get a good extraction with Bet (brain is
> excluded top
> and bottom). We have been dealing with this issue by correcting for
> the
> bias field with Fast and have gotten good results. Since Fsl-vbm
> applies
> Bet we have entered bias-corrected scans into our Vbm analyses.
> However,
> will this cause problems when segmentation is done in
> fslvbm_2_template (or
> anywhere else in Fsl-vbm)?
The bias correction is fine, but if you have already run BET that
might compromise the FSL-VBM when you feed the already-betted image
into FSL-VBM. The simple solution is to apply the bias field
correction to the original image and feed that into FSL-VBM. That
should be fine then.
> Also, is it best to use the bias-corrected scans in First as well?
> It seems
> possible that not correcting scan intensities for the bias field will
> interfere with the identification of structures (since First uses
> intensities in this process), thanks,
If it looks like the bias field correction has improved the image then
it should be better to feed the corrected image into FIRST than the
original.
Cheers, Steve.
>
> Jeff
>
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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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