> I ran dicom import, realignment (motion correction) and slice timing
> correction for each session separately already. Do you mean I now run
> the realignment routine with the reslice only option, with as input
> the slice timing corrected images from each session? or should I skip
> the first insession realignment altogether and do the realignment with
> images from all sessions?
Ideally, you should have run the realignment with both sessions together.
Specify the files as different sessions (runs) for the same subject, and it
should bring the images into closer alignment with each other.
> No, I coregistered the mean functional to the anatomical in each case,
> by wiggling the mean functional around (source image), and I asked spm
> to keep my slice timing corrected images coregistered with the mean
> functional image. However, your first point (across sessions
> realignment) might do the trick, by better matching the orientations
> compared to my coregistration of both sessions to the same anatomical
> image. Although, my images seemed pretty well coregistered before
> normalization, and the coregistration algorithm and the realignment
> algorithm are pretty similar, aren't they?
The coregistration and realignment algorithms are related, but the objective
functions are different (to allow registration between modalities) and the
accuracy of the realignment (within modality) may be slightly higher.
I still think Check Reg should be the best option for figuring out what may
have gone wrong. Compare the mean fMRI of the two sessions with each other
to see how well aligned they are.
Best regards,
-John
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