> Does first-level analysis need to be conducted within AFNI?

No, most programs in AFNI including 3dLME can take NIfTI files as input.

> it only contains 2 subjects, as I wanted to be sure it worked before including them all!

This is at least one source for model failure: there is not enough data available for the model. Try the script with at least 10 subjects.

In addition, a couple of other potential issues:

1) It seems that Time_dif varies within subject. So, you may consider a finer model:

-model 'Visit*Time_dif+Base_DD+Base_Age' \\
...
-ranEff '~1+Time_dif'

2) Be careful about the centering issue. If the group average of Time_dif varies across those three visits, you may have to center within each visit first before feeding those Time_dif values into the data table for 3dLME:

[afni.nimh.nih.gov]

3) The following part

-num_glf 1 \
-glfLabel 1 'Main_effect_visit' -glfCode 1 ' Visit : 1*v1 -1*v2 & 1*v1 -1*v3' \

is unnecessary because 3dLME automatically provides an omnibus test for each variable in the model.

Gang



Edited 1 time(s). Last edit at 06/13/2018 12:25PM by Gang.