Hi,
On 17 Sep 2007, at 13:26, Ged Ridgway wrote:
> Hi Steve,
>
>>> 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?
>
> Well, it's a bit of a long story, but essentially I had a good semi-
> automatic brain-mask (GM+WM only) for the first time-point, but not
> for the second. I thought that a slightly dilated version of the
> first brain-mask might be a more reasonable thing to use for the
> second time-point than a BET mask, which is quite different in
> character (includes CSF, and often includes some neck/eyes/
> whatever; though bet_robust might fix that).
>
> My main concern with my approach was that by overwriting BET's
> brain_masks I'd mess something up that I'd overlooked (e.g. in
> siena_cal or one of the other parts, but I can't think of anything
> obvious). My other concern was that the no-CSF masks could give a
> very sharp drop from GM/WM intensities to zero (especially if the
> semi-automatic mask is too tight anywhere) compared to a BET mask
> dropping gradually from partial-volumed brain tissue down to
> partial-volumed CSF; I worried this might screw up the correlation
> analysis.
Yes, the use of the same dilated mask for timepoint 2 should be ok,
but I would be more concerned if the mask excludes CSF as you might
not end up with a good tissue-type segmentation and might not end up
with an optimal set of brain/non-brain edge points.
Cheers.
>
>> I would run SIENA both ways (with its own betting and yours)
>> with -d and compare each stage carefully
>
> Fair enough, I'd started to do that, but thought I should check
> that I hadn't missed something stupid. I'll post a follow-up if I
> find anything interesting...
>
> Cheers,
> Ged.
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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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