Dear SPMers,
I've been trying to preprocess some functional data using SPM2. I noticed
that after normalizing the data (I coregistered the T1 to the mean image,
then used the T1 to estimate parameters with respect to a CCHMC template),
that some superior slices are partially black, as if a black circle or oval
have blocked out brain data. I also noticed that in some of my data, the
mean resliced image created during realignment (nothing else was resliced)
looks like it was "shaved" off at the top of the brain because there was a
diagonal black line (as if the rest of the brain superiorly was outside the
field of view). Maybe the normalization process made more superior slices
black due to interpolation...
So my question is this: How does this affect my analysis? Are those slices
excluded from my analysis? And how can I remedy this problem?
Just so you know, I used the same bounding box as that of the template. I've
tried different voxel sizes as well.
Should I be turning off the masking during realignment? Should I be using
the brainmask that came with the CCHMC template for normalization, or is
that just for segmentation?
Or can I just continue preprocessing the data?
I'd love to hear your responses. I thank you in advance.
~V
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