Hi, Sondos-

The heterogeneity of such (esp. since the individual level results are usually quite noisy in FMRI) can make challenges. Note that having different numbers of ROIs won't cause errors in 3dNetCorr or 3dTrackID per se; however, trying to combine matrices of different sizes after those steps would present challenges, indeed. Those analyses are typically based on looking at "connections" between the same two targets across a group (whether those be correlation values or tract-derived estimates); therefore, having different targets to start with would not really fit with this approach.

Two ways to go might be:
1) from the individual-level results, only keep ROIs that are common across subjects.
2) map the group-level ROIs to each subject and use those for tracking/netcorring.

--pt