Hello again!
I failed to mention in my first email that I used -c and -r options
before. It did give me a better extraction. Those images, however,
caused alignment problems when used in SPM5. I tried to realign the
extracted image but it simply would not work. Am I missing a step?
Also, when I used -f ang -g options on both cropped and uncropped
images, I lost some brain volume. What is an acceptable brain volume
loss?
Thanks again!
Iris Bautista
On 7/13/06, Steve Smith <[log in to unmask]> wrote:
> Hi,
>
> On 12 Jul 2006, at 22:44, iris bautista wrote:
>
> > Hello FSL Users,
> >
> > I have been using BET v1.2 in FSL 3.3 on Linux Redhat9 to strip my
> > structural images that will be used for VBM analysis but several
> > problems occured.
> >
> > 1) First I kept the fractional threshold at 0.5, but some non-brain
> > tissue remained (as seen on
> > https://webspace.utexas.edu/ieb58/MPRAGE1-CG1013_brain.jpg). It was
> > eliminated after changing the threshold to 0.6 but I lost too much
> > brain volume. Is it better to leave it at 0.55 even with the extra
> > tissue to preserve brain volume? I'm not sure if the extra tissue
> > would result in innacurate data in my analysis.
> >
> > 2) Since changing the threshold did not work, I used avwroi to crop
> > the original image which resulted in a decent extraction. However,
> > after overlaying the extracted image on the original, part of the
> > cerebellum was lost (as seen on
> > https://webspace.utexas.edu/ieb58/avMPRAGE1-CG1013_overlay2.jpg). How
> > much brain volume loss is acceptable when studying structural images?
>
> Instead of using avwroi you could also use the -c option to tell BET
> where to center the starting estimate - this has the advantage of
> still being in the original space then. On the other hand, when you
> crop an image to remove unnecessary slices at the bottom, that's
> generally a good thing to do as you rarely want to keep them anyway.
> On your cropped image have you tried using the -f and the -g options?
> Looks like you should be able to get a bit of an improvement, though
> it does look pretty good already.
>
> > 3) I still used the image from step 2 on SPM5 in MATLAB 7.0 to see if
> > it would cause any problems. I first used the "check register" button
> > to check the alignment of the stripped template (using BET with 0.5
> > threshold) with the image from step 2. The images, however, do not
> > align even after I reoriented the extracted brain. I'm not sure what
> > else to do at this point.
>
> You can try the above and see if that fixes this too - it may be that
> this problem relates to the setting of a coordinate origin.
>
> Cheers, Steve.
>
> >
> > Thank you for your help!
>
>
> ------------------------------------------------------------------------
> ---
> 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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