Hi,
We are attempting to create a average brain template in SPM2 for the
subjects in our study (~30 children), following a method similar to that
of Marko Wilke et al (2002). We plan to use this for coregistration and
normalization of our functional data (rigid body registration from
individual T1 to individual EPI, then regular affine/non-linear
transformation from individual T1 to the new template T1, applying the
parameters to the EPI). This has been our method so far:
1) 12-parameter affine transformation (with brain mask, as used by
Wilke) from individual high-resolution T1 images to the MNI T1
template.
2) Realigning using a coregister and reslice, creating a mean image of
all the individual normalized anatomicals, and smoothing that to create
the template.
Wilke also discussed using an intensity nonuniformity correction.
Why is this step necessary in the creation of the template? Our
purposes are for "better normalization" of our functional data by using
a template that corresponds better to the individual subjects; since we
are not comparing anatomical differences between subjects, could this
step be omitted? Also, is it problematic for brain averaging if the
mean intensities of the images are not identical? I read Chris Rorden's
MRIcro tutorial that in the final release of SPM99, the normalization
precedure automatically matches the image brightness - if that is the
same for SPM2, then did an intensity normalization already happen during
the affine transformation?
Another thing is that we would like to be able to report the results
in Talairach space. This could be as simple as an affine/non-linear
transform from the new template to the MNI T1 template, but I am
hesitant to apply 2 transforms to our functional data, effectively
smoothing it twice over. Is there some way in SPM to get the parameters
for the [individual T1 -> new template T1 -> MNI template T1]
transformation, such as multiplying the matrices of the 2 transforms,
and apply those parameters to the individual EPI?
Thanks for all the help!
Daniel Simmonds
Developmental Cognitive Neurology
Kennedy Krieger Institute
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