3dMVM set up


I am attempting to set up a code to utilize 3dMVM and I have a few questions below regarding this set up. I would like to complete a Group (2) x Phase (2) x Reinforcement (2) x Subjects (38) ANOVA, and I have an unequal number of participants within each group. Before, I tried to use GroupAna, but realized I could not run this program as I have too many factors and had an unbalanced design.

(1) Do the input files need to include the participant’s IDs? I got these input files by using 3dcalc to separate the resulting stats file from 3dDeconvolve into the separate conditions
(2) I am not too sure what the main difference between using the glf and glt is, and I have noticed that some of the examples on the website do not include the “glf”. I have indicated the different interactions and main effects I am interested in using the glt.
(3) Does the general set up of the code looks correct (pasted below)? I have not listed all my participants yet. I have used the examples in the AFNI webpage and other threads from the message board to guide my set up.

Thank you in advance for your assistance.


My code is:
3dMVM -prefix group -jobs 2
-bsVars group
-wsVars ‘phasereinf’
-SS_type 2
-num_glt 15
-gltLabel 1 3way_inter -gltCode 1 'group : 1
pat -1ctrl phase: 1acq -1rev reinf : 1corr -1incor’
-gltLabel 2 group_phase -gltCode 2 'group : 1
pat -1ctrl phase: 1acq -1rev’
-gltLabel 3 group_reinf -gltCode 3 'group : 1
pat -1ctrl reinf: 1corr -1incor’
-gltLabel 4 phase_reinf -gltCode 4 'phase : 1
acq -1rev reinf : 1corr -1incor’
-gltLabel 5 group -gltCode 5 'group : 1
pat -1ctrl’
-gltLabel 6 phase -gltCode 6 'phase : 1
acq -1rev’
-gltLabel 7 reinf -gltcode 7 'reinf : 1
corr -1incorr’
-gltLabel 8 acq_group -gltcode 8 'phase : 1
acq group : 1pat -1ctrl’
-gltLabel 9 rev_group -gltcode 9 ‘phase : 1rev group : 1pat -1ctrl’
-gltLabel 10 corr_group -gltcode 10 'reinf : 1
corr group : 1pat -1ctrl’
-gltLabel 11 incor_group -gltcode 11 ‘reinf : 1incor group : 1pat -1ctrl’ \
-gltLabel 12 acq_reinf -gltcode 12 'phase : 1
acq reinf : 1corr -1incor’ \
-gltLabel 13 rev_reinf -gltcode 13 ‘phase : 1rev reinf: 1corr -1incor’
-gltLabel 14 corr_phase -gltcode 14 'reinf : 1
corr phase: 1acq -1rev’
-gltLabel 15 incor_phase -gltcode 15 ‘reinf : 1incor phase: 1acq -1*rev’
Subj group phase reinf InputFile
6292 pat acq corr 6292/SS_proc_6292_FIRST_3RUNS_Sep4.results/RevP_acq_corr_fed+tlrc
6292 pat acq incor 6292/SS_proc_6292_FIRST_3RUNS_Sep4.results/RevP_acq_incor_fed+tlrc
6292 pat rev corr 6292/SS_proc_6292_FIRST_3RUNS_Sep4.results/RevP_rev_corr_fed+tlrc
6292 pat rev incor 6292/SS_proc_6292_FIRST_3RUNS_Sep4.results/RevP_rev_incor_fed+tlrc
8225 pat acq corr 8225/SSwarp_proc_8225_FIRST_Sep4.results/RevP_acq_corr_fed+tlrc
8225 pat acq incor 8225/SSwarp_proc_8225_FIRST_Sep4.results/RevP_acq_incor_fed+tlrc
8225 pat rev corr 8225/SSwarp_proc_8225_FIRST_Sep4.results/RevP_rev_corr_fed+tlrc
8225 pat rev incor 8225/SSwarp_proc_8225_FIRST_Sep4.results/RevP_rev_incor_fed+tlrc

(1) Do the input files need to include the participant’s IDs?

Yes, any characters including numbers such as those in your 3dMVM script would be fine as long as they can differentiate the subjects.

(2) I am not too sure what the main difference between using the glf and glt is

GLT is pretty much all you need. GLF is mainly for cases when you want to examine the differences across three or more levels of a factor.

(3) Does the general set up of the code looks correct (pasted below)?

You need a backslash () for the following line in your 3dMVM script:

-SS_type 2 \

Type 3 is more popular.

Thank you very much for the clarification! I ran my code successfully and it seemed to work.

I was reviewing the 3dMVM post and I saw that for the gltCoding it indicated:

"…for example, the following ‘Group : 1A -1B & 1A -1C’ tests the main effect across the 3 groups A, B, and C. Important Note: this option is only valid for
a hypothesis that involves between-subjects variables. For an F-test involving a within-subject variable, use -glfCode with 3dLME instead

In my ANOVA I have one between factor and 2 within-subjects factors. When I listed my glts I had indicated the main effects of each factor and their interactions. From the posting above, it would seem incorrect for me to use 3dMVM and get main effects for the within-subject factor? I am just wondering whether this is the case, or whether this would be okay.

Thank you in advance for your help.


All those post hoc tests with gltCode in your 3dMVM script are fine. The sentence you quoted from the 3dMVM help is meant to refer to the usage of glfCode, not gltCode.