From visual inspection, I would tend to agree that that is a pretty
awful spatial normalisation. How did you actually achieve that
result? Did you do it via coregistering with an anatomical and
segmenting that to get the normalisation parameters (as suggested by
your Dicom>nifti>realign>coregister>segment>normalize>smooth workflow)
or did you use the Normalise button to match with the EPI template in
SPM?
I'd guess that the fMRI are pretty distorted relative to the
anatomical data. If this is the case, then you are not likely to
achieve an accurate rigid-body alignment between functional and
structural. This could mess up any spatial normalisation via the
structural.
There is also quite a lot of intensity nonuniformity in your fMRI, as
well as a bit of a difference between the image contrast and that of
the EPI template. Both of these would mean that least-squares
matching between your fMRI and the EPI template may not work so well.
Have you tried to see how well the segmentation works when applied
directly to the EPI?
Best regards,
-John
On 19 October 2011 17:14, Meghana Mehta <[log in to unmask]> wrote:
> We’ve been running our processing and analysis steps through SPM8 and are
> noticing an odd result. Briefly, the processing steps are typical for
> SPM8, as detailed in the tutorial auditory data set in the SPM8 manual:
>
> Dicom>nifti>realign>coregister>segment>normalize>smooth
>
> We then calculate t-maps at the individual subject level for each contrast
> of interest.
>
> We’ve found that the resulting individual subject normalized image is
> smaller than the template image. We’ve searched through the archives and so
> far have found two threads that appear to describe a similar effect,
> although these seem to describe this shrinkage at the group level. Subject
> motion is one issue that is commented on in these previous threads, but this
> seems less likely for our scans, since we have excluded subjects with
> excessive motion.
>
> http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind02&L=SPM&P=R117479&I=-3&d=No+Match%3BMatch%3BMatches
>
> http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind05&L=SPM&P=R309800&I=-3&d=No+Match%3BMatch%3BMatches
>
> We’ve included a check reg pdf that shows, in order from left to right and
> top to bottom, the initial raw subject nifti image, the realigned subject
> nifti image, the normalized subject nifti image, the smoothed subject nifti
> image, and the t-map of block on versus fixation for that same subject.
> We’ve also included the SPM8 EPI template that the individual subject’s
> scans are normalized to for comparison at the bottom right.
>
> We have specifically noticed shrinkage in the occiptal cortex as can be seen
> on the pdf.
>
> Any help with this issue is highly appreciated
>
> Thanks and Regards
>
> Meghana
>
>
>
>
>
>
>
>
>
>
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