Hi Stefano.
> I am attempting to do a segmentation starting from 2 channels, a proton
> density weighted and a T2 weighted image, but I get too much grey matter in
> places where white matter should be. Steve, I am now working from the same
> images I sent you recently. I was able to extract the brain, and after noise
> reduction the images look much better. Also, registration of either image to
> a T1 weighted image acquired on a 3T scanner (rather than 1.5), does not
> work well at all, when T1 weighted images from 1.5 register fine. Which
> parameters should I play with in the advanced options for registration to
> have this work? Any suggestions? Stefano
Hi - when I tried registering the brain-extracted versions of the images
that you sent (including the T2-weighted) to a high res that I have from
the 3T here these work fine with the default FLIRT settings. You may be
having problems due to the fact that I think your slice thickness is set
too small in your images - it needs increasing by around a factor of 1.5?
If you can't get this to work ok then feel free to email me the reference
image you are working with.
Thanks, Steve.
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