afni.nimh.nih.gov

You can do the pairwise correlations with 3dTcorrelate and then Gang is finishing up work on 3dISC, the group level analysis program, but he may be willing to send you a less pretty script that will do the LME part of things.

There's also the BrainIAK project which has group analysis ISC methods. It's fairly easy to do this from the pairwise steps from AFNI as well.