Hi David,
With regard to 1):
- what you do (when I understand you correctly) will coregister your T1
weighted structural image to the mean functional image (it is better to
not reslice during realignment when you plan to normalize your
functional scans as well). And because your mean functional is logically
in register with your realigned functionals, the realigned functionals
are also in register with your T1. You can subsequently choose your
fuctionals as 'images to write' at normalization stage, and base your
parameters on the T1>MNI warp.
"When mozes does not come to the mountain, the mountain will have to
come to Mozes".
Cheers,
Bas
David Kideckel schreef:
> Dear fellow SPMers:
>
> I have a couple of questions for the preprocessing steps in SPM5:
>
> 1) For coregistration: If I coregister using the mean functional
> image (produced in estimate and reslice in realignment) as my
> "reference image" and my T1 as my "source image" this won't coregister
> all my functionals to the anaTomic, but rather only the mean one,
> right? If so, then does this mean that my functionals are not in
> registration with anything? This is slightly confusing, because if
> what I have said is true, then when I normalize my images, when I
> select all the functionals, I will be normalizing uncoregistered
> functional scans. The same would go for smoothing too. To solve this,
> is it wise select the the fMRI scans as well as "other images?"
>
> 2) For segmentation/normalization: If I am not normalizing to an MNI
> template (eg EPI in SPM5 template directory, as I would do if I didn't
> do segmentation), but rather to the parameters estimated in the
> segmentation process, is this sufficient to normalize my T1 and
> functional scans into MNI space? Or is there an added step?
>
> If any of the above is not not clear, please let me know and I will
> try and reword.
>
> Thanks.
>
> David
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Dr. S.F.W. Neggers
Division of Brain Research
Rudolf Magnus Institute for Neuroscience
Utrecht University Medical Center
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