# 3dANOVA3

I’m running a 3dANOVA3 with two groups (HVs & patients), with three resting state runs per participant (1,2,3) and looking for an effect over time/runs (presumably fatigue). It’s not clear to me from the AFNI help text what the difference is between type 4 and type 5 in the model, and what is meant by “C(A)” for type 5? Here’s the help text on the type option:
3dANOVA3
-type k type of ANOVA model to be used:
k = 1 A,B,C fixed; AxBxC
k = 2 A,B,C random; AxBxC
k = 3 A fixed; B,C random; AxBxC
k = 4 A,B fixed; C random; AxBxC
k = 5 A,B fixed; C random; AxB,BxC,C(A)

I’d appreciate any details and helpful references. Thanks.

what the difference is between type 4 and type 5 in the model,

Type 4 is for a two-way ANOVA with both factors A and B as within-subject (or repeated-measures) factors. In Type 5, factor A is a between-subject factor.

what is meant by “C(A)” for type 5?

It means that each subject of factor C is nested within one of the levels (groups; e.g., male/female) of factor A.

Use type 5 in your case. However, 3dANOVA3 requires that all groups of factor A have exactly the same number of subjects. If you have an unequal number of subjects across groups, use 3dMVM.