I don't see how this procedure should have changed your functional data. This
should have stayed in exactly the same orientation etc as it was prior to the
coregistration.
> I am using SPM2, and after coregistration, I see that functional image is
> pitched backward, and the crosshair is migrated 5-10mm away from the
> anterior commissure on the structural. The crosshair migration might be do
> to my lack of skill in finding the AC when reorienting the functional image
> (!), but not sure why the functional is pitched backward after this
> coregistration step. Here are the steps I take:
>
> Number of Subjects: 1
> Which option: Coregister and reslice
> Choose target image: click on the mean image from the realignment
> Choose source image: choose the structural (usually mprage) image for this.
> Other images: simply press done, without selecting any images.
>
> Are there any obvious problems here? My preprocessing steps include slice
> timing correction, reorienting, realigning, coregistration, normalisation,
> smoothing. Is coregistration necessary?
Coregistration is sometimes necessary. If you want the fMRI and anatomical
data to be in register, then it is necessary. If you want to estimate how to
warp the subjects fMRI datato MNI space, using warps estimated from the the
anatomical data, then it is also necessary.
If you don't plan to use the anatomical image, then coregistration is not
necessary.
Best regards,
-John
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