Hi - you'll have to try this, but the bias didn't look very bad. Note that
you _may_ be able to use BET and FAST (with -or option) to correct bias.
Without seeing your original (non-masked) input image I can't give much
more advice on what mmight work!
Cheers, Steve.
On Fri, 29 Oct 2004, Martin Kavec wrote:
> Dear Steve,
>
> when you look at the images do you think that at least the RF bias field is
> corrected sufficiently? In the other words, provided that the images cover
> "enough" brain, would normalized mutual information (eventually other) cost
> function work on these images?
>
> Is there any other approach (though not implemented in FSL) to register these
> type of images, which in your oppinion could work. I know, my questions depart
> from FSL, nevertheless, I would appreciate your expert opinion?
>
> Best wishes,
>
> 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
> >
>
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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