Hi - yes, it makes sense that if you need 12DOF to get a good
registration then FLIRT won't be happy with using 6!
I think you can maybe get what you're asking for by using 12DOF,
saving the transform then using the -fixscaleskew option in
convert_xfm, using an identity transform matrix as the second matrix.
This may work ok for you.
Wrt the cost function - yes, you'll just have to try alternative cost
functions to see whether they help on your particular data.
Cheers, Steve.
On 3 Jul 2006, at 10:40, Ged Ridgway wrote:
> Hi,
>
> I'm using FLIRT to register T1 structurals to avg152T1. If I use
> full 12 dof affine, then the results look beautiful. However, for
> complicated reasons, I'd like to just use 6 dof rigid transforms,
> and FLIRT seems much less successful at this (all same options
> except dof; mostly defaults, e.g. correlation ratio, etc).
>
> I suppose this makes sense, because the subjects don't match avg152
> well in terms of overall brain scale (they are elderly/Alzheimer's)
> or local things such as ventricular size. But is there anything I
> might try to improve things?
>
> I can't use a 12 dof as a starting point for a second 6dof run, can
> I? Since I'll still end up with effectively 12 dof. I assume I
> can't just take a 12 dof matrix, break it down into skew/scale/rot/
> trans and just "reset" the skew and scale? I'm guessing this would
> give peculiar results with e.g. the rotation that was derived to
> happen after some scalings being off without them, but perhaps I'm
> wrong about this?
>
> I guess since I'm doing T1-T1, I should perhaps be using normcorr,
> rather than corratio? The contrast in my images didn't seem that
> close to avg152T1, which was why I stuck with an inter-modal cost
> function, but perhaps an intra-modal one would be better in the
> face of slight imperfections due to the scaling problem? I gather
> (N)MI can have quite a sharp basin in the cost function, perhaps
> corratio suffers similarly, with slight mismatch being no better
> than yards away?
>
> I open to any suggestions, however random they might seem!
>
> Many thanks,
> Ged.
------------------------------------------------------------------------
---
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
------------------------------------------------------------------------
---
|