This analysis method is effective but antiquated.

The method of using lags with binary stim_files (and especially -stim_nptr) has been replaced with use of TENT functions. For details, please see the handout for the "Deconvolution" bootcamp class:
AFNI class: Deconvolution

For an example of the current processing style, consider reviewing the handout for the "Soup to Nuts" bootcamp class:
AFNI class: Start To Finish

HowTo 05 : Group Analysis - AFNI 3dANOVA2

background : experiment - overview of the experiment, data and analysis
ANOVA - overview of Analysis of Variance

Linux scripts : @analyze_ht05 - script for individual subject analysis
@anova_ht05 - script for group analysis

main help pages: AFNI_howto_subject - explanation of the shell script: subject analysis
AFNI_howto_group - explanation of the shell script: group analysis

download : ht05_html.tgz - download script and html pages
ht05_full.tgz - download everything (includes data : 500 Megabytes!)

              This HowTo is based on the paper:

              Beauchamp, M.S., Lee, K.E., Haxby, J.V., & Martin, A. (2003).
                  FMRI responses to video and point-light displays of moving
                  humans and manipulable objects.
                  Journal of Cognitive Neuroscience, 15:7, 991-1001.