> We initially used a FOV in our EPI sequence resulting in some (larger) brains being cut off at the parietal and frontal lobules. We then increased the slice thickness to account for this. The problem is when we do the second level analysis; only voxels which are present in every subject seems to be included, resulting in a loss of data mainly in the parietal lobule which we are interested in. Is there any way to include voxels that are only present in some subjects (treating the rest as missing data points) or do we have to throw away some of our subjects?
I can think of two options:
1) Discard the subjects with partial-brain coverage, and report all
analyses on the same group of subjects (that include parietal regions
you are interested in);
2) Perform two sets of analyses: one on the full group (for regions
that all subjects have data), and a second restricted to the subset of
subjects that have full brain coverage.
I think (1) will be much more straightforward. It's appropriate that
SPM enforces data in all subjects for second level analyses, because
this ensures the correct number of degrees of freedom, as well as
having identical statistical models for all voxels.
Also, it sounds like you may have changed your scanning sequence to
achieve a larger FOV—does (1) also mean that all subjects will have
received the identical scanning sequence? This would also probably
make interpretation slightly easier (as you woudn't have to be
concerned with any potential differences introduced by scanning
Hope this helps!
Dr. Jonathan Peelle
Department of Neurology
University of Pennsylvania
3 West Gates
3400 Spruce Street
Philadelphia, PA 19104