Thanks so much for the help! I used 3dcalc to get the difference and followed Example 1. The model will run and gives me an Fstat and mean/tstat's for all of the time points, but the sub-bricks for the GLTs are all zero. Why would this be? I tried several of the 3dLME examples in AFNI_data6/GroupAna_cases to see if there were a problem with my R installation, but they all ran fine and produced outputs.

Here's the command I'm using. The subbricks for 'FourTimePoints' and 'ExampleTTest' are all zero.

3dLME -prefix myOutput_S00minusS01 -jobs 8 \
-mask maskFile+tlrc \
-model '0+Time' \
-qVars Order \
-qVarCenters 0 \
-ranEff '~1' \
-dbgArgs \
-corStr 'Order : AR1' \
-SS_type 3 \
-num_glf 1 \
-glfLabel 1 'FourTimePoints' \
-glfCode 1 'Time : 1*Diff03 & 1*Diff04 & 1*Diff05 & 1*Diff06' \
-num_glt 1 \
-gltLabel 1 'ExampleTTest' \
-gltCode 1 'Time : 1*Diff05 +1*Diff06' \
-dataTable Subj Time Order InputFile \
Y4_P0204 Diff00 00 /work/Trey/diffTentHDR/S00minusS01/S00minusS01.Y4_P0204+tlrc.HEAD[00] \
Y4_P0204 Diff01 01 /work/Trey/diffTentHDR/S00minusS01/S00minusS01.Y4_P0204+tlrc.HEAD[01] \
...

Thanks,
Trey