Dear Janet and Rosalia,
> Based on your comment, I will skip entering the timeseries of the lesioned area as a nuisance covariate.
I didn't say you should necessarily skip it ;-) I remarked that one needs to be a little careful, especially if the lesioned area is one that in a healthy brain ones task would elicit activation.
> For the affine transform, can I use one of the .mat files that is produced in the original feat? If so, I assume this would be "highres2standard.mat"?
Yes, that is the one you want.