Dear Steve,
thanks a lot for your opinion and suggestion to erode the images. Your
conclusion reveals hard facts which is not making me happier.
:)
On the other hand it suggests where to go further, which is invaluabe.
:)
Thanks again and have a nice weekend.
Martin
Quoting Stephen Smith <[log in to unmask]>:
> Hi - the idea of using the input image here as it's own weighting mask
> is
> a good one, given that it's outline has gotten seriously corrupted. I
> would erode the mask a couple of times though to really get rid of
> edge
> effects (using -ero in avwmaths).
>
> HOWEVER, this particular input image really is totally screwed and
> even
> the above probably can't be made to work; whatever preprocessing was
> carried out removed huge amounts of brain, so you don't stand much
> chance
> of registering to the reference. Really, you need to go back and fix
> the
> preprocessing!
>
> Cheers, Steve.
>
>
>
> On Fri, 29 Oct 2004, Martin Kavec wrote:
>
> > Hello group,
> >
> > I have no luck to register a high resolution T1-weighted (1.5T)
> volume
> > (stored at http://www.uku.fi/~kavec/reference_brain.tar.gz ) and
> > T1-weighted (0.12T) volume (stored at
> > http://www.uku.fi/~kavec/input_brain_bias.tar.gz ).
> >
> > Problematic is, I believe, the input volume.
> > (1) It was masked by the manufacturer of the MR system with an
> ellipsoid
> > mask to hide artefacts due to B0 inhomogeneities. The mask
> > introduces false boundaries in the image, which confuses
> > registration.
> > (2) Additionally, the images were acquired with a
> > large diameter surface coil producing large intensity variations,
> which
> > I did my best to correct using FAST.
> >
> > To address (1), I am created a brain mask (stored at
> > http://www.uku.fi/~kavec/input_brain_mask.tar.gz ) using BET and I
> use
> > this as an input weighting volume.
> >
> > I would expect that normalize mutual information should be able to
> > register the imaged using DOF=6-9, but after failing in this I tried
> > virtually every combination of DOF<6 and cost function, but as I
> mentioned
> > without any good results.
> >
> > I would appreciate any input as to what am I doing wrong. Many thanks
> in
> > advance.
> >
> > Martin
> >
>
> --
> 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
>
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