Hi!

Assuming an experiment where the subjects get two different stimuli A and B. We are interested in the contrast between A and B: C=A -B.

Normally we would have run this via afni_proc.py and defined the contrast using:

-gltsym 'SYM: A -B' \
-glt_label C \

This would give each subject's stats file a sub-brik with the t-score from a t-test with null: C = 0 where C = A-B.

Let's say we run 20 subjects and and we procede to the group level analyis. We would then run 3dttest++ where the input would be, for each subject, the coefficient for the contrast (should simply be beta(A)-beta(B) from the regression):

3dttest++ -prefix C \
-setA \
stats.sub01+tlrc[C#0_Coef] \
stats.sub02+tlrc[C#0_Coef] \
...
stats.sub20+tlrc[C#0_Coef] \

Is there any statistical/theoretical difference between doing this and using the -AminusB command in 3dttest++? In this example it would be:

3dttest++ -prefix C -paired -AminusB \
-setA \
stats.sub01+tlrc[A#0_Coef] \
stats.sub02+tlrc[A#0_Coef] \
...
stats.sub20+tlrc[A#0_Coef] \
-setB \
stats.sub01+tlrc[B#0_Coef] \
stats.sub02+tlrc[B#0_Coef] \
...
stats.sub20+tlrc[B#0_Coef] \

Are these methods doing the SAME things? Or do we in some way treat the variance differently?

If these methods are the same it would be much more flexible to use the latter method since you don't have to re-run the afni_proc.py function the add another contrast.

Thanks!