I can't speak to the exclusions of lesions via a mask for CONN analysis, but our group has used a few packages for lesion segmentation with the SPM-based Lesion Segmentation Toolbox (LST) being one of the better packages.  No lesion segmentation approach is perfect (except for tight manual tracing), but LST does a reasonably good job and importantly for our purposes has longitudinal modules.

I would be interested to hear from others about lesion masks in the CONN processing pipeline.  Is there an option during the preprocessing set-up to allow for masks?

Warm regards,
Jeff