Sophia,
Theoretically speaking, the repeated-measures (or within-subject) ANOVA for one group you ran in FSL should be the same as a paired t-test. Are you comparing such a paired t-test from FSL with one of the post hoc test from 3dLME? If so, one possibility about the discrepancy is the following: You can *only* perform one-sided (or one-tailed) t-test in other software packages. It is debatable whether such a blindsight approach is valid or not, but the default in AFNI is two-sided unless the user knowingly switches to one-sided testing on the AFNI GUI.
Gang
Edited 1 time(s). Last edit at 05/30/2017 05:28PM by Gang.