basic 2 x 2 design question

AFNI Message Board
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AFNI version info (afni -ver):
Version AFNI_25.2.12 'Gordian I

Dear AFNI Board,

I hope this message finds you well.

I have been reviewing the message board and AFNI Bootcamp videos, but I am still having difficulty deciding on the most appropriate analysis path for my study. I am working with a 2 × 2 design, with:

2 groups (experimental vs. control),
2 time points (pre- vs. post-intervention),
22 participants total(11 per group).

The analysis is whole-brain, and I am interested in:

  1. Within-subject pre/post differences,
  2. Within-group pre/post differences,
  3. Between-group main effects of group, time, and their interaction.

My current plan is:

Use 3dcalc for individual within-subject pre/post comparisons.
Use 3dttest++ -paired for within-group comparisons across the 11 subjects. I wonder, though: would 3dMEMA be more appropriate than 3dttest++? (I do have REML results from afni_proc.py.)
For the between-group analyses (the full 2×2 design), I am considering a two-way ANOVA. The more I read, the more uncertain I become about the best approach—whether to use 3dLMEr, 3dANOVA, or another option I have not explored yet.

I would be very grateful for your guidance on the most suitable analysis path for this design.

Thank you very much for your time and help!

Kind regards,
Aude.

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Aude,

There are several ways to analyze your data. You might consider two relatively straightforward options: 3dMVM and 3dLMEr. For the latter, you can find useful guidance in this blog post.

Gang Chen

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Thank you very much Gang!
Kind regards,
Aude.