It looks very much as if it is going wrong, but there is not enough
information here to know why. There are lots of possibilities, but the more
likely ones are:
1) Segmentation didn't work well, possibly because of poor initial
registration. Take a look at a spatially normalised GM image produced by the
segmentation. This will tell you how well this step has worked.
2) User error. If the anatomical scans that were segmenented got moved
afterwards. If you segment the anatomical, and then coregister it to some
other image (so that it is treated as the "source" image or one of the
"other" images), then things will be messed up.
Best regards,
-John
On Saturday 29 November 2008 00:41, Julien Dubois wrote:
> Dear list,
> I want to do some statistics at the group level, hence I have to work
> in the MNI space. However, on inspection of the normalization results,
> I see that the subjects' normalized anatomicals don't match well, and
> actually that they don't match the MNI template well (which is why
> they don't match well...). I believe I'm using the recommended steps:
> segment, make sure origin is close enough to AC, then use segmentation
> parameters to estimate non-linear warping parameters. I attach here
> results for 2 subjects: T1.png is the bias-corrected anatomical for
> the first subject; normalizedT1_vs_templateT1.png is the result of
> normalization compared to the MNI template. Same for second subject,
> with _2 at the end of the filename.
> Is this kind of result expected, or is there clearly something going
> wrong (that's my hunch)? does any have an idea of what I should do to
> make it better?
> - Julien
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