I have one participant, whose brain I cannot seem to be able to
coregister. I have four runs of an experimental paradigm. I
have reoriented the anatomical image, and reoriented all of the
functional images based on a reorientation I performed for the
final scan of the second run to the EPI template. I then
realigned the functional images to the final scan in the second
run, and resliced the mean image only. I tried to coregister
the mean functional image to the anatomical, but the anatomical
image is always higher than the mean functional image. I have
tried to reorient the functional images and re-run the
realignment on the altered functional images, but no matter how
much I move my functional images upwards, the coregistration
process always gives me the same output (the anatomical image
being much higher than the mean functional image). This only
seems to happen with one participant, I haven’t encountered a
coregistration error with any other participant.
Probably the easiest fix for this would be to use the Segment button
(maybe the New Segment of SPM8) to generate native space tissue class
images of GM, WM and CSF, as well as a bias corrected version of your
anatomical scan. The c1, c2 and c3 images could be used to skull strip
the bias corrected anatomical scan, which should give you an image that
coregisters rather better.
The skull stripping bit can be done using ImCalc, where you would select
the m***.img, c1***.img, c2***.img and c3***.img. The expression to
evaluate would then be i1.*((i2+i3+i4)>0.5) .
If you plan to use the ***_seg_sn.mat file for spatially normalising,
then you should coregister the functional data to the output of ImCalc.
This would be done by having the ImCalc result as "reference", one of
the fMRI scans as the "source", and all the others as "other".
Best regards,
-John
--
John Ashburner <[log in to unmask]>
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