Dear Moyra,
> I have conducted VBM analyses in SPM8 both with and without the use of a
> mask. The issue I am facing is that I am encountering blobs outside the
> brain (see figure 1 for results without a mask and figure 2 for results
> with a mask).
>
> The images were processed using the DARTEL protocol and the mask was
> normalized to the SPM T1 template.
>
> I have checked the mask by overlaying it onto the T1 template and it
> appears to fit perfectly.
First, you are quite correct to assume that when using an appropriate
mask in the same space as the images you are analyzing, you should not
get results outside of this mask - so there indeed seems to be a bit of
a puzzle here.
It would help to know a little bit more about how you processed the
structural images in DARTEL. Did you normalize to MNI space? Have you
checked the DARTEL-normalized structural images to make sure they show
good correspondence with MNI space (based on the templates included with
SPM, for example)? If not, then you may have a mask that is in MNI
space, but results which are not, which is not a good situation to be in.
Second, it would be helpful to know how you created your explicit mask,
and to see that mask overlaid along with the (unmasked) results, in MNI
space - this will give a good idea of which blobs the mask will end up
removing.
Finally, what threshold did you use for your results? I ask because it's
a bit odd that there appear to be some *additional* results in the
masked analysis (figure2.JPG) that were not in the unmasked analysis -
such as what looks to be in the cerebellum. At a consistent voxelwise
threshold I would not expect this to happen.
Hope this helps!
Best regards,
Jonathan
--
Dr. Jonathan Peelle
Center for Cognitive Neuroscience and
Department of Neurology
University of Pennsylvania
3 West Gates
3400 Spruce Street
Philadelphia, PA 19104
USA
http://jonathanpeelle.net/
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