Hi Paul,

> Could i use these two t maps from separate analysis approaches with 3ddot to
> investigate the relationship between GM structure covariance and GM atrophy ?

3ddot with its option '-demean' does seem to fit your scenario. However, I would avoid computing the correlation with t-statistic values, if possible. Instead some direct measure that carries some physical meaning would be preferred.

> In addition, if i have two binary maps, whether i can use 3ddot to investigate the
> relationship between two binary images ?

That sounds a little shaky because the typical correlation measure is more about two continuous variables. However, you may consider Phi coefficient (see here: [en.wikipedia.org]) for which 3ddot should work fine.

Gang