Kim,

The error is generated when the VOI region extends beyond the first level
mask.

There are a few options:
(1) Multiple the VOI by the group mask, this will ensure that the VOI
doesn't not extend beyond the useable data in each subject. ** This may or
may not work for native space as you'd have to transform the VOI to native
space.
(2) Set P.equalroi=0 and P.FLmask=1; this will allow unequal sized ROI and
allow them to be trimmed by the 1st level mask.

Different sized VOIs:
I have not tested the effect of different VOI sizes across subjects. If the
VOIs are similar in size, then I think the effects should be minimal. If
one VOI is 100 voxels and another VOI is 10 voxels, then I think there
could be an effect of VOI size.

The key isn't the VOI size, but the signal of the VOI. If the signal is
homogenous throughout the VOI, then the size will have no effect. If the
signal is heterogenous, then the size will have an effect; especially if
one part of the VOI is missing in one group of subjects compared to another
group of subjects.

Hope this helps.

-Donald