> That would be useful if storing data in a few masks. If I understand you correctly, then for my problem it would yield a large amount of duplication of data (as each voxel may be contained in hundreds of ROIs). For a few ROIs with little overlap it may indeed be more efficient though to use a sparse representation.
The formats seem equivalent and inter-convertable to me so I either must not have explained it clearly or I really don't understand what you're trying to compute. I don't see why there would ever be any duplication using either approach (even in the presence of extensive overlap).
I was mostly concerned about keeping track of the position of each mask because I was thinking about this from an image filtering point of view. Anyway, it sounds like you're pretty clear about where you want to go with this.
Cheers,
--judd