Hi! I have some questions regarding 3dMVM and if it's set up correctly...


We have data from patients who get treatment (REAL vs SHAM) and they watch stimuli (pictures of ALOHOL vs Non-ALCOHOL). In previous analysis I have used 3dMVM since the groups are uneven. Typically like this:

3dMVM -prefix no_covariates -dataTable @table.txt -jobs 10 \
-mask mask+tlrc \
-bsVars Treatment \
-wsVars Stim \
-num_glt 3 \
-gltLabel 1 Treatment \
-gltCode 1 'Treatment: 1*real -1*sham' \
-gltLabel 2 Stim \
-gltCode 2 'Stim: 1*alc -1*non_alc' \
-gltLabel 3 TreatmentXStim \
-gltCode 3 'Treatment: 1*real -1*sham Stim: 1*alc -1*non_alc'

With the table:

Subj Treatment  Stim  InputFile 
S01    real    alc  stats.subject_01_REML+tlrc.BRIK'[alc#0_Coef]' 
S01    real    non_alc     stats.subject_01_REML+tlrc.BRIK'[non_alc#0_Coef]'
S02    sham    alc   stats.subject_02_REML+tlrc.BRIK'[alc#0_Coef]' 
S02    sham    non_alc    stats.subject_02_REML+tlrc.BRIK'[non_alc#0_Coef]'

Now we also want to add some covariates (of interest), e.g. some scores they give after treatment with relate to the success of the treatment. These are just numbers. So I added -qVars. Would this be between subject variable? Or within?

New mvm script:

3dMVM -prefix covariates -dataTable @table_plus_covariates.txt -jobs 10 \
-mask mask+tlrc \
-bsVars "Treatment+AUQ1" \
-qVars "AUQ1" \
-wsVars Stim \
-num_glt 3 \
-gltLabel 1 Treatment \
-gltCode 1 'Treatment: 1*real -1*sham' \
-gltLabel 2 Stim \
-gltCode 2 'Stim: 1*alc -1*non_alc' \
-gltLabel 3 TreatmentXStim \
-gltCode 3 'Treatment: 1*real -1*sham Stim: 1*alc -1*non_alc'

New table:

Subj Treatment  Stim AUQ1  InputFile 
S01    real    alc   10.3 stats.subject_01_REML+tlrc.BRIK'[alc#0_Coef]' 
S01    real    non_alc 10.3    stats.subject_01_REML+tlrc.BRIK'[non_alc#0_Coef]'
S02    sham    alc   11.1 stats.subject_02_REML+tlrc.BRIK'[alc#0_Coef]' 
S02    sham    non_alc  11.1 stats.subject_02_REML+tlrc.BRIK'[non_alc#0_Coef]'

As output, regarding the qvar, I only get the F-score for AUQ1 (related to variance explained by AUQ1 when accounting for all the other variables as well?) and the interaction between AUQ1 and Stim (AUQ1:Stim F). Why don't I also get the interaction between AUQ1 and treatment?

To summarize:
Is the script + table correct for this experiment?
Is the qvar in this case within of between subject variable?
Meaning of AUQ1 F?
Why don't I get AUQ1:Treatment, but only get AUQ1:Stim?

Thanks so much in advance!