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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