Dear Paul,
Initially you asked only about registration without mentioning
segmentation. So our original answers were about registration
and not segmentation. However, Gwen is totally right - do not
do any registration before segmentation. We always recommend
doing segmentation first, then doing registration and then applying
the transformation to the segmentation outputs to get them into
standard space (if that is what you need).
You may be getting confused with how to apply standard space
priors in segmentation. This requires a registration first, in order
to get the appropriate transformation to standard space, but
when you run the segmentation you use the original image
(not any transformed version) and, in addition, the transformation
matrix (which is used to transform the standard space priors
into the same space as the original image). I hope this helps to
clarify things a bit.
All the best,
Mark
On 23 Nov 2010, at 19:55, SUBSCRIBE FSL Anonymous wrote:
> hi Gwen,
> Please realize that I am very New At this!! But,, are you sure,, i have been taught to always register (using FLIRT) my subject to a standard template prior to segmentation (using FAST), what Mark or Matt said was to use FNIRT instead of FLIRT, you are saying don't register any subject(s) prior to segmentation??? wow!
> paul
>
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