Hello Alfonso,

Thank you for getting back to me.  Sorry for my slow response back.  

The issue is that the values from a between-groups conn analysis (2 groups, two beta images) don't match up with the values from the same roi in the t-con contrast image (group 1 > group 2) or the subject-specific rZ values from the firstlevel folder.  Instead, they correspond closely with the eigenvariate....  

Hopefully that clarifies the issue and why I am confused...

Happy to elaborate further.

Thanks for the help,
Patrick