3dMVM/3dLME error

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1

Hi Gang,
I want to run a group analysis with 1 between subject factor: GROUP (Main, Control), and 2 with subject factors: TASK (Video, Language), VISIT (1st, 2nd, 3rd). There are missing data for some within-subject factors.
I was trying the following “3dMVM” and “3dLME” commands but got similar error information that I don’t understand. Could you please help? Thank you very much!

3dMVM -prefix ./GroupLevelAnova -jobs 10
-mask ./BrainMask.nii.gz
-bsVars ‘GROUP’
-wsVars ‘TASKVISIT’
-wsE2
-num_glf 6
-glfLabel 1 Main_Video_Training -glfCode 1 'GROUP : 1Main TASK : Video VISIT : 12nd -11st & 13rd -11st’
-glfLabel 2 Main_Language_Training -glfCode 2 ‘GROUP : 1Main TASK : Language VISIT : 12nd -11st & 13rd -11st’
-glfLabel 3 Control_Video_Training -glfCode 3 'GROUP : 1Control TASK : Video VISIT : 12nd -11st & 13rd -11st’
-glfLabel 4 Control_Language_Training -glfCode 4 ‘GROUP : 1Control TASK : Language VISIT : 12nd -11st & 13rd -11st’
-glfLabel 5 Main-Control_Video_Training -glfCode 5 'GROUP : 1Main -1Contol TASK : Video VISIT : 12nd -11st & 13rd -11st’
-glfLabel 6 Main-Control_Language_Training -glfCode 6 'GROUP : 1Main -1Control TASK : Language VISIT : 12nd -11st & 13rd -11st’
-num_glt 18
-gltLabel 1 Main_Video_1st -gltCode 1 'GROUP : 1Main TASK : 1Video VISIT : 11st’
-gltLabel 2 Main_Video 2nd -gltCode 2 ‘GROUP : 1Main TASK : 1Video VISIT : 12nd’
-gltLabel 3 Main_Video 3rd -gltCode 3 'GROUP : 1Main TASK : 1Video VISIT : 13rd’
-gltLabel 4 Main_Language_1st -gltCode 4 ‘GROUP : 1Main TASK : 1Language VISIT : 11st’
-gltLabel 5 Main_Language 2nd -gltCode 5 'GROUP : 1Main TASK : 1Language VISIT : 12nd’
-gltLabel 6 Main_Language 3rd -gltCode 6 ‘GROUP : 1Main TASK : 1Language VISIT : 13rd’
-gltLabel 7 Control_Video_1st -gltCode 7 'GROUP : 1Control TASK : 1Video VISIT : 11st’
-gltLabel 8 Control_Video_2nd -gltCode 8 ‘GROUP : 1Control TASK : 1Video VISIT : 12nd’
-gltLabel 9 Control_Video_3rd -gltCode 9 'GROUP : 1Control TASK : 1Video VISIT : 13rd’
-gltLabel 10 Control_Language_1st -gltCode 10 ‘GROUP : 1Control TASK : 1Language VISIT : 11st’
-gltLabel 11 Control_Language_2nd -gltCode 11 'GROUP : 1Control TASK : 1Language VISIT : 12nd’
-gltLabel 12 Control_Language_3rd -gltCode 12 ‘GROUP : 1Control TASK : 1Language VISIT : 13rd’
-gltLabel 13 Main-Control_Video_1st -gltCode 13 'GROUP : 1Main -1Control TASK : 1Video VISIT : 11st’
-gltLabel 14 Main-Control_Video_2nd -gltCode 14 'GROUP : 1Main -1Control TASK : 1Video VISIT : 12nd’
-gltLabel 15 Main-Control_Video_3rd -gltCode 15 'GROUP : 1Main -1Control TASK : 1Video VISIT : 13rd’
-gltLabel 16 Main-Control_Language_1st -gltCode 16 'GROUP : 1Main -1Control TASK : 1Language VISIT : 11st’
-gltLabel 17 Main-Control_Language_2nd -gltCode 17 'GROUP : 1Main -1Control TASK : 1Language VISIT : 12nd’
-gltLabel 18 Main-Control_Language_3rd -gltCode 18 'GROUP : 1Main -1Control TASK : 1Language VISIT : 1*3rd’
-dataTable
Subj GROUP TASK VISIT InputFile
…

Error in seq.default(2, length(sepTerms), 2) :
wrong sign in ‘by’ argument
Calls: process.MVM.opts → gl_Constr → glfConstr → seq → seq.default
Execution halted

3dLME -prefix ./GroupLevelAnova -jobs 10
-mask ./BrainMask.nii.gz
-model ‘GROUPTASKVISIT’
-ranEff ‘~1’
-SS_type 3
-num_glf 6
-glfLabel 1 Main_Video_Training -glfCode 1 ‘GROUP : 1Main TASK : Video VISIT : 12nd -11st & 13rd -11st’
-glfLabel 2 Main_Language_Training -glfCode 2 'GROUP : 1Main TASK : Language VISIT : 12nd -11st & 13rd -11st’
-glfLabel 3 Control_Video_Training -glfCode 3 ‘GROUP : 1Control TASK : Video VISIT : 12nd -11st & 13rd -11st’
-glfLabel 4 Control_Language_Training -glfCode 4 'GROUP : 1Control TASK : Language VISIT : 12nd -11st & 13rd -11st’
-glfLabel 5 Main-Control_Video_Training -glfCode 5 ‘GROUP : 1Main -1Contol TASK : Video VISIT : 12nd -11st & 13rd -11st’
-glfLabel 6 Main-Control_Language_Training -glfCode 6 ‘GROUP : 1Main -1Control TASK : Language VISIT : 12nd -11st & 13rd -11st’
-num_glt 18
-gltLabel 1 Main_Video_1st -gltCode 1 ‘GROUP : 1Main TASK : 1Video VISIT : 11st’
-gltLabel 2 Main_Video 2nd -gltCode 2 'GROUP : 1Main TASK : 1Video VISIT : 12nd’
-gltLabel 3 Main_Video 3rd -gltCode 3 ‘GROUP : 1Main TASK : 1Video VISIT : 13rd’
-gltLabel 4 Main_Language_1st -gltCode 4 'GROUP : 1Main TASK : 1Language VISIT : 11st’
-gltLabel 5 Main_Language 2nd -gltCode 5 ‘GROUP : 1Main TASK : 1Language VISIT : 12nd’
-gltLabel 6 Main_Language 3rd -gltCode 6 'GROUP : 1Main TASK : 1Language VISIT : 13rd’
-gltLabel 7 Control_Video_1st -gltCode 7 ‘GROUP : 1Control TASK : 1Video VISIT : 11st’
-gltLabel 8 Control_Video_2nd -gltCode 8 'GROUP : 1Control TASK : 1Video VISIT : 12nd’
-gltLabel 9 Control_Video_3rd -gltCode 9 ‘GROUP : 1Control TASK : 1Video VISIT : 13rd’
-gltLabel 10 Control_Language_1st -gltCode 10 'GROUP : 1Control TASK : 1Language VISIT : 11st’
-gltLabel 11 Control_Language_2nd -gltCode 11 ‘GROUP : 1Control TASK : 1Language VISIT : 12nd’
-gltLabel 12 Control_Language_3rd -gltCode 12 'GROUP : 1Control TASK : 1Language VISIT : 13rd’
-gltLabel 13 Main-Control_Video_1st -gltCode 13 ‘GROUP : 1Main -1Control TASK : 1Video VISIT : 11st’
-gltLabel 14 Main-Control_Video_2nd -gltCode 14 ‘GROUP : 1Main -1Control TASK : 1Video VISIT : 12nd’
-gltLabel 15 Main-Control_Video_3rd -gltCode 15 ‘GROUP : 1Main -1Control TASK : 1Video VISIT : 13rd’
-gltLabel 16 Main-Control_Language_1st -gltCode 16 ‘GROUP : 1Main -1Control TASK : 1Language VISIT : 11st’
-gltLabel 17 Main-Control_Language_2nd -gltCode 17 ‘GROUP : 1Main -1Control TASK : 1Language VISIT : 12nd’
-gltLabel 18 Main-Control_Language_3rd -gltCode 18 ‘GROUP : 1Main -1Control TASK : 1Language VISIT : 13rd’
-dataTable
Subj GROUP TASK VISIT InputFile
…

Error in seq.default(2, length(sepTerms), 2) :
wrong sign in ‘by’ argument
Calls: process.LME.opts → gl_Constr → glfConstr → seq → seq.default
Execution halted

2

Zhi-Hao,

What is your AFNI version?

afni -ver

Try updating your AFNI first. If the error persists, could you post some context of the data table (e…g., with at least 8 lines representing the 8 possible combinations among the 3 factors)?

3

Hi Gang,
My AFNI has just been updated earlier this month for the newly added feature of autocorrelation modeling in 3dClustSim. So I assume the version is fine:
Precompiled binary linux_xorg7_64: Aug 2 2016 (Version AFNI_16.2.07)

Please find below part of the data table (lengthy data path omitted):

Subj GROUP TASK VISIT InputFile
ID023 Control Video 1st t10_AM2coefNwarp2mm.nii.gz
ID023 Control Video 2nd t10_AM2coefNwarp2mm.nii.gz
ID023 Control Video 3rd t10_AM2coefNwarp2mm.nii.gz
ID014 Main Video 1st t10_AM2coefNwarp2mm.nii.gz
ID014 Main Video 2nd t10_AM2coefNwarp2mm.nii.gz
ID014 Main Video 3rd t10_AM2coefNwarp2mm.nii.gz
ID023 Control Language 1st t10_AM2coefNwarp2mm.nii.gz
ID023 Control Language 2nd t10_AM2coefNwarp2mm.nii.gz
ID023 Control Language 3rd t10_AM2coefNwarp2mm.nii.gz
ID014 Main Language 1st t10_AM2coefNwarp2mm.nii.gz
ID014 Main Language 2nd t10_AM2coefNwarp2mm.nii.gz
ID014 Main Language 3rd t10_AM2coefNwarp2mm.nii.gz \

4

OK, there are two types of errors in your script:

  1. The word ‘Contol’ in the following should be ‘Control’.

-glfLabel 5 Main-Control_Video_Training -glfCode 5 ‘GROUP : 1Main -1Contol TASK : Video VISIT : 12nd -11st & 13rd -11st’ \

  1. You forgot to add coefficients for the levels of factor TASK:

-glfLabel 1 Main_Video_Training -glfCode 1 ‘GROUP : 1Main TASK : 1Video VISIT : 12nd -11st & 13rd -11st’
-glfLabel 2 Main_Language_Training -glfCode 2 ‘GROUP : 1Main TASK : 1Language VISIT : 12nd -11st & 13rd -11st’
-glfLabel 3 Control_Video_Training -glfCode 3 ‘GROUP : 1Control TASK : 1Video VISIT : 12nd -11st & 13rd -11st’
-glfLabel 4 Control_Language_Training -glfCode 4 ‘GROUP : 1Control TASK : 1Language VISIT : 12nd -11st & 13rd -11st’
-glfLabel 5 Main-Control_Video_Training -glfCode 5 ‘GROUP : 1Main -1Control TASK : 1Video VISIT : 12nd -11st & 13rd -11st’
-glfLabel 6 Main-Control_Language_Training -glfCode 6 'GROUP : 1Main -1Control TASK : 1Language VISIT : 12nd -11st & 13rd -11st’ \

Also, I’m not so sure whether 3dMVM/3dLME gives proper F-tests for a within-subject factor like all these six tests specified through GLF. Could you let me know how they pan out for 3dMVM as well as 3dLME?