Dear Karen,
You should use 6 DOF for functional to structural registration within the same subject (ideally with BBR). Also, make sure you are being consistent with brain extraction, as registrations between one brain-extracted and one non-brain-extracted image often end up with incorrect scalings.
I hope this helps.
If not, let us know.
All the best,
Mark
On 17 Mar 2014, at 20:58, Karen Moffat <[log in to unmask]> wrote:
> Hello Mark,
>
> Regarding my Alzheimer's dataset and the image registration , I got another strange issue.
> After image registration of my functional to structural then to MNI, it seems my functional images are quite smaller than a normal brain !!!!!!! They look like a brain but a small brain comparing to my structural images.
> How do I say that? I did the isotropic resampling my functional data and structural to 2 mm. Then I displayed them on FSLVIEW and saw that my functional image are smaller than structural one and doesn't cover each other !!! I think the image registration between func and struct has not been perfectly done. In the preprocessing I used 12 DOF for both registration steps . I really appreciate if you can share your thoughts with me.
>
> Thanks,
>
> Karen
>
>
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