For a long time the lack of 2nd-order contrast testing in 3dANOVA3 has largely prevented people from using the group analysis program for 2-way within-subject / repeated-measures ANOVA (3dANOVA3 -type 4) and 2-way mixed-effects ANOVA (3dANOVA3 -type 5). That is no longer the case. We recently added two new options in 3dANOVA3, -aBcontr and -Abcontr, for types 4 and 5 with the following usage:
-aBcontr c_1 c_2...c_a : j contrast_label -- 2nd order contrast in factor A, at fixed B level j
-Abcontr i : c_1 c_2...c_b contrast_label -- 2nd order contrast in factor B, at fixed A level i
We also modified options -amean, -bmean, -adiff, -bdiff, -acontr and -bcontr in 3dANOVA3 based on the same modification principles announced almost one month ago:
<[afni.nimh.nih.gov];
The newly released AFNI package will reflect the above modifications, and the relevant statistics will be provided in a new version of 3dANOVA2 and 3dANOVA3 manuals in the near future.
Gang