AIR 5.x is fully compatible with any .air files derived using AIR 1.0. However, the reverse is not the case. The old AIR 1.0 programs will not be able to read the new .air files. If you start getting error messages complaining about being unable to read or load .air files, check your path and make sure that an old version of AIR is not being called without your realizing it.
The most difficult adjustment in starting to use AIR 5.x is the fact that a single program, alignlinear, now provides the automated alignment for linear intrasubject, intersubject, and intermodality problems. As a result, you must pay close attention to make sure that you always specify the model, thresholds, and partitions appropriately. You may find it easiest to use the Tcl/Tk graphical user interface to choose the various options.