Hi Ged,
On 6 Sep 2007, at 12:26, Ged Ridgway wrote:
> Dear Steve,
>
> I've been trying SIENA on data for which I have manually segmented
> brain masks (for one, or possibly both time-points). These masks
> trace around the tissue that is either GM or WM; CSF is not
> included. Obviously I don't have BET-style skull estimates for
> input to pairreg.
>
> Following some work Bea Sneller did:
> http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0703&L=FSL&P=R20435
> I've been trying the following simple approach:
> * let SIENA call BET as usual (getting skull estimates etc.)
> * overwrite BET's _brain_mask images with my masks
> - if only one mask is available, dilate this mask to provide an
> over-generous mask for the second image
Not sure what you mean - why would only one be available? You need
two input images and SIENA runs BET on both, so why would you not at
least have those?
> * it appears to me from siena_diff.cc that the new _brain_masks
> should be handled correctly (transformed to the half-way space,
> etc.), but I might be missing something?
>
> The render images resulting from this have really nice looking edge
> locations, without the non-brain tissue that occasionally gets
> included by BET. So far so good...
>
> However, the actual values of final PBVC don't seem as good as the
> BET results (based on some simulated atrophy images with
> approximately known volume loss) even though BET has not worked
> that perfectly on some of the images.
>
> So, am I missing something that is wrong with my approach? One
> thing I'm wondering at the moment, is that the tight (no-CSF) brain
> masks could give a sharp discontinuity at the edges (especially if
> the manual segmentation actually went inside the brain slightly, by
> mistake), which perhaps doesn't give the best results with
> siena_diff's correlation of the intensity profiles. If this is the
> case, I guess it would be better to dilate both brain-masks by some
> amount. I'm intending to try this, but I thought I'd check first
> whether there is anything else I might be missing...
I can't think of anything obvious - if you're just playing with the
lines near the start of SIENA that do the betting then this should be
fairly straightforward. I would run SIENA both ways (with its own
betting and yours) with -d and compare each stage carefully if you
want to see where the difference is happening. Sorry not to have
anything more useful to suggest!
> Thanks in advance for your help,
>
> Ged.
>
> P.S. I'm under the impression that the SIENA pipeline (including
> BET, FLIRT, etc.) is unchanged from FSL 3.3 to 4, is that correct?
I think so, yes. I'm pretty sure that the only main change was the
generation of the web page report etc.
Cheers.
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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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