Dear Varina,
The red lines are *supposed* to come from the other image in the pair.
If they came from the same image they would tell you nothing about
the registration quality. The whole idea is to see if the red lines from
one image correspond to changes in intensity in the other (grayscale)
image underneath.
Your results look fine to me, although the brain extraction seems
to have gone wrong in the inferior frontal portion (unless 2yo brains
are strange - I must admit that I am no expert in pediatric brains).
I would check the brain extraction though, and see if you are happy
with it.
It might also help you to work through some of the FSL course material
and see what the results look like there (where they are representative
of good, if slightly dated, results).
All the best,
Mark
On 10 Sep 2011, at 19:53, Varina Wolf wrote:
> FMRIB Upload: 962586
>
> Hi,
>
> Sorry to bother you all again about my registration. It did improve with increasing the DOF.
>
> On close inspection it appears that the top and bottom images are mirrors of what should be registered to that image. I mean, for example, look at the entire row on top compared to the bottom, the red squiggly lines that should outline the features of the brain are those of the image below it and not the one that it is overlayed onto. This is most obvious over the sagital temporal lobe images and coronal cerebellum images. This is true in all three sets of pictures. What is going on? What should I do?
>
> This occured regardless of the use of the MNI 152 or MNI 2yo standard image.
>
> Most Gratefully,
> Varina
>
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