I’m a beginner in AFNI and trying to evaluate, with 3dDeconvolve “-nodata” mode, the time series generated by RFSgen. According to the “afni_howto” tutorial, under the circumstance of 3 experimental conditions (A, B, and C), 3 GLT’s are needed (contrasts of AB, AC, and BC).

Now my problem is that I have 6 conditions (say, A to F). Then how should I do the GLT’s? Contrasts between each pair (AB, AC, …, EF), each triplet (ABC, ABD, …, DEF), or between each combination with 4 or more conditions? Or all above?

Or, is it so that I don’t need the glt option actually? If so, by what do I compare the qualities of different time series?

I know this question may be simple but it’s really annoying me and I would appreciate any help. Thanks!

PS. Here is my code without adding the glt option (only showing the 3dDeconvolve part; 10 repetitions for each condition):

```
3dDeconvolve \
-nodata 150 2.0 \
-nfirst 3 -nlast 149 \
-polort A \
-num_stimts 6 \
-stim_file 1 "RSF.0001.1D[0]" -stim_label 1 S1 \
-stim_file 2 "RSF.0001.1D[1]" -stim_label 2 S2 \
-stim_file 3 "RSF.0001.1D[2]" -stim_label 3 S3 \
-stim_file 4 "RSF.0001.1D[3]" -stim_label 4 S4 \
-stim_file 5 "RSF.0001.1D[4]" -stim_label 5 S5 \
-stim_file 6 "RSF.0001.1D[5]" -stim_label 6 S6 \
> 3dD.nodata.0001
```

and here’s the screen output:

++ using NT=150 time points for -nodata

++ Imaging duration=300.0 s; Automatic polort=3

++ Number of time points: 150 (before censor) ; 147 (after)

- Number of parameters: 10 [4 baseline ; 6 signal]

++ ----- Signal+Baseline matrix condition [X] (147x10): 1.46989 ++ VERY GOOD ++

++ ----- Signal-only matrix condition [X] (147x6): 1 ++ VERY GOOD ++

++ ----- Baseline-only matrix condition [X] (147x4): 1.08516 ++ VERY GOOD ++

++ ----- polort-only matrix condition [X] (147x4): 1.08516 ++ VERY GOOD ++

++ +++++ Matrix inverse average error = 2.36283e-16 ++ VERY GOOD ++

++ Matrix setup time = 0.00 s

and the file:

Stimulus: S1

h[ 0] norm. std. dev. = 0.3394

Stimulus: S2

h[ 0] norm. std. dev. = 0.3451

Stimulus: S3

h[ 0] norm. std. dev. = 0.3531

Stimulus: S4

h[ 0] norm. std. dev. = 0.3509

Stimulus: S5

h[ 0] norm. std. dev. = 0.3423

Stimulus: S6

h[ 0] norm. std. dev. = 0.3410