"model test failed" - errors in 3dLME, 3dMVM

Hello again,

I’ve figured out recently how to install missing R packages to make 3dMVM run (I had a post on that here a few weeks ago).
The surprising thing, is that after it already worked and after I tried various models with 3dMVM, it stopped working.

It seems like I have a syntax error, although I am using scripts that have already proven to work.
I thought maybe it has to do with some R packages again, but I don’t know. I am really lost.
When I run rPkgsInstall -pkgs ALL -check, I get this:


These packages are not installed on the computer: brms!

And I don’t think this is relevant for 3dMVM.

In 3dMVM, I ran the exact same script I used before (from the terminal).
I also tried 3dLME, and I get this error in diary.txt:


~~~~~~~~~~~~~~~~~~~ Model test failed  ~~~~~~~~~~~~~~~~~~~
Possible reasons:

0) Make sure that R packages nlme and phia have been installed. See the 3dLME
help documentation for more details.

1) Inappropriate model specification with options -model, or -qVars.

2) Incorrect specifications in general linear test coding with -gltCode.

3) Mistakes in data table. Check the data structure shown above, and verify
whether there are any inconsistencies.

4) Inconsistent variable names which are case sensitive. For example, factor
named Group in model specification and then listed as group in the table header
would cause grief for 3dLME.

** Error: 
   Quitting due to model test failure...

Here is the LME script (I suppose whatever the error is, it is the same for 3dMVM):


3dLME -prefix LME_GROUP_LEVEL_contrasts_fluency2 -jobs 2 \
-model "Morph+Root_fluency+Phon_fluency" \
-qVars "Root_fluency, Phon_fluency" \
-ranEff '~Morph' \
-SS_type 3 \ 
-num_glt 2 \
-gltLabel 1 RootFluency_effect -gltCode 1 'Morph : 1*words -1*scrambled Root_fluency :' \
-gltLabel 2 PhonFluency_effect -gltCode 2 'Morph : 1*words -1*scrambled Phon_fluency :' \
-dataTable \
Subj    Sex     Age    WM      	MIE  	Phon_fluency   Root_fluency 	Morph 		InputFile \
S05 	male  	30    7.25 	0.226   49 		29 		words  		S05.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S05 	male  	30    7.25 	0.226   49   		29 		scrambled  	S05.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S03 	male 	28    6.00 	0.2248  37 		29 		words 		S03.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S03 	male 	28    6.00 	0.2248  37 		29 		scrambled 	S03.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S04 	male 	34    6.00 	0.3673  56 		27 		words 		S04.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S04 	male 	34    6.00  	0.3673  56 		27 		scrambled 	S04.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S07 	female 	24    6.50  	0.1125  41 		21 		words 		S07.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S07 	female 	24    6.50  	0.1125  41 		21 		scrambled 	S07.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S08 	male 	24    6.75 	0.119   47 		24 		words 		S08.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S08 	male 	24    6.75 	0.119   47 		24 		scrambled 	S08.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S09 	male 	26    6.00 	0.1767  56 		24 		words 		S09.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S09 	male 	26    6.00 	0.1767  56 		24 		scrambled 	S09.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S14 	male 	30    7.00 	0.0637  47 		35 		words 		S14.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S14 	male 	30    7.00 	0.0637  47 		35 		scrambled 	S14.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S12 	male 	24    4.75 	0.399   52 		34 		words 		S12.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S12 	male 	24    4.75 	0.399   52 		34 		scrambled 	S12.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S10 	female 	24    5.50 	0.1258  36 		32 		words 		S10.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S10 	female 	24    5.50 	0.1258  36 		32 		scrambled 	S10.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S11 	female 	25    5.00 	0.3598  36 		28 		words 		S11.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S11 	female 	25    5.00 	0.3598  36 		28 		scrambled 	S11.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S16 	female 	34    5.25 	0.1167  51 		31 		words 		S16.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S16 	female 	34    5.25 	0.1167  51 		31 		scrambled 	S16.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S13 	female 	30    7.25 	0.241   29 		39 		words 		S13.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S13 	female 	30    7.25 	0.241   29 		39 		scrambled 	S13.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S15 	male 	28    7.50 	0.0925  60 		51 		words 		S15.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S15 	male 	28    7.50 	0.0925  60 		51 		scrambled 	S15.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S19 	female 	27    5.75 	0.1159  46 		31 		words 		S19.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S19 	female 	27    5.75 	0.1159  46 		31 		scrambled 	S19.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S18 	male 	25    4.75 	0.1808  50 		35 		words 		S18.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S18 	male 	25    4.75 	0.1808  50 		35 		scrambled 	S18.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S20 	female 	27    6.50 	0.1276  45 		32 		words 		S20.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S20 	female 	27    6.50 	0.1276  45 		32 		scrambled 	S20.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S22 	female 	22    5.25 	0.1018  37 		29 		words 		S22.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S22 	female 	22    5.25 	0.1018  37 		29 		scrambled 	S22.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S23 	female 	26    6.00 	0.1453  46 		38 		words 		S23.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S23 	female 	26    6.00 	0.1453  46 		38 		scrambled 	S23.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S38 	female 	31    4.75 	0.092   68 		38 		words 		S38.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S38 	female 	31    4.75 	0.092   68 		38 		scrambled 	S38.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S24 	female 	21    5.25 	0.113   30 		20 		words 		S24.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S24 	female 	21    5.25 	0.113   30 		20 		scrambled 	S24.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S25 	female 	33    5.00 	0.1435  28 		19	 	words 		S25.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S25 	female 	33    5.00 	0.1435  28 		19	 	scrambled 	S25.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S27 	female 	27    7.25 	0.3087  44 		35 		words 		S27.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S27 	female 	27    7.25 	0.3087  44 		35 		scrambled 	S27.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S28 	female 	21    6.50 	0.3086  40 		26 		words 		S28.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S28 	female 	21    6.50 	0.3086  40 		26 		scrambled 	S28.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S31 	female 	23    4.25 	0.1218  17 		25	 	words 		S31.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S31 	female 	23    4.25 	0.1218  17 		25 		scrambled 	S31.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S34 	male 	27    6.00 	0.1976  54 		32 		words 		S34.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S34 	male 	27    6.00 	0.1976  54 		32 		scrambled 	S34.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S29 	female 	24    6.75 	0.1501  42 		28 		words 		S29.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S29 	female 	24    6.75 	0.1501  42 		28 		scrambled 	S29.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S26 	female 	21    6.75 	0.1446  46 		38 		words 		S26.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S26 	female 	21    6.75 	0.1446  46 		38 		scrambled 	S26.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S30 	female 	24    6.25 	0.1889  45 		27 		words 		S30.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S30 	female 	24    6.25 	0.1889  45 		27 		scrambled 	S30.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S43 	female 	20    6.00 	0.1816  39 		35 		words 		S43.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S43 	female 	20    6.00 	0.1816  39 		35 		scrambled 	S43.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S33 	male 	27    7.00 	0.1703  43 		27 		words 		S33.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S33 	male 	27    7.00 	0.1703  43 		27 		scrambled 	S33.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S32 	female 	30    6.75 	0.1353  37 		40 		words 		S32.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S32 	female 	30    6.75 	0.1353  37 		40 		scrambled 	S32.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S36 	male 	24    4.25 	0.1452  38 		27 		words 		S36.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S36 	male 	24    4.25 	0.1452  38 		27 		scrambled 	S36.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S35 	female 	21    5.25 	0.0276  32 		30 		words 		S35.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S35 	female 	21    5.25 	0.0276  32 		30 		scrambled 	S35.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S39 	female 	24    5.75 	0.067   59 		37 		words 		S39.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S39 	female 	24    5.75 	0.067   59 		37 		scrambled 	S39.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S37 	female 	23    5.75 	0.1906  34 		25 		words 		S37.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S37 	female 	23    5.75 	0.1906  34 		25 		scrambled 	S37.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S47 	male 	24    6.00 	0.1217  47 		29 		words 		S47.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S47 	male 	24    6.00 	0.1217  47 		29 		scrambled 	S47.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S40 	female 	27    6.50 	0.1938  36 		34 		words 		S40.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S40 	female 	27    6.50 	0.1938  36 		34 		scrambled 	S40.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S41 	female 	22    5.00 	0.237   45 		40 		words 		S41.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S41 	female 	22    5.00 	0.237   45 		40 		scrambled 	S41.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S45 	male 	30    7.00 	0.1566  60 		41 		words 		S45.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S45 	male 	30    7.00 	0.1566  60 		41 		scrambled 	S45.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S42 	female 	21    5.75 	0.1215  36 		30 		words 		S42.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S42 	female 	21    5.75 	0.1215  36 		30 		scrambled 	S42.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S44 	female 	31    6.75 	0.1588  57 		35 		words 		S44.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S44 	female 	31    6.75 	0.1588  57 		35 		scrambled 	S44.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \
S46 	female 	32    5.00 	0.191   40 		25 		words 		S46.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \
S46 	female 	32    5.00 	0.191   40 		25 		scrambled 	S46.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]'

The R package ‘brms’ is only relevant to two recent programs, MBA and BayesianGroupAna.py, not 3dMVM/3dLME.

I suggest that you use 3dMVM in this case because you have a typical ANCOVA. And make sure that you declare the variable ‘Morph’ as a within-subject variable.

-gltLabel 1 RootFluency_effect -gltCode 1 ‘Morph : 1words -1scrambled Root_fluency :’
-gltLabel 2 PhonFluency_effect -gltCode 2 ‘Morph : 1words -1scrambled Phon_fluency :’ \

These two tests don’t make sense with the model you specified:

-model “Morph+Root_fluency+Phon_fluency” \

If you assume that no interaction exists between ‘Morph’ and ‘Root_fluency’, then why are you requesting for those two tests? You may consider a model like

-model “MorphRoot_fluency+MorphPhon_fluency” \

Gang, thank you for the reply!
Is MVM still the right thing to do, even if I am interested in the covariate (i.e. Root_Fluency and Phon_Fluency), while controlling for the categorical variable (Morph)?
Also, when trying to run 3dMVM I still get an error. This is my script:


3dMVM -prefix MVM_GROUP_LEVEL_fluency2 -jobs 2 \
-wsVars Morph \
-bsVars "Root_fluency+Phon_fluency" \
-qVars "MIE,Root_fluency,Phon_fluency,WM,Age" \
-num_glt 2 \
-gltLabel 1 RootFluency_effect -gltCode 1 'Morph : 1*words -1*scrambled Root_fluency :' \
-gltLabel 2 PhonFluency_effect -gltCode 2 'Morph : 1*words -1*scrambled Phon_fluency :' \
-dataTable \
Subj    Sex     Age    WM      	MIE  	Phon_fluency   Root_fluency 	Morph 		InputFile \ 
S05 	male  	30    7.25 	0.226   49 		29 		words  		S05.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S05 	male  	30    7.25 	0.226   49   		29 		scrambled  	S05.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S03 	male 	28    6.00 	0.2248  37 		29 		words 		S03.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S03 	male 	28    6.00 	0.2248  37 		29 		scrambled 	S03.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S04 	male 	34    6.00 	0.3673  56 		27 		words 		S04.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S04 	male 	34    6.00  	0.3673  56 		27 		scrambled 	S04.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S07 	female 	24    6.50  	0.1125  41 		21 		words 		S07.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S07 	female 	24    6.50  	0.1125  41 		21 		scrambled 	S07.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S08 	male 	24    6.75 	0.119   47 		24 		words 		S08.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S08 	male 	24    6.75 	0.119   47 		24 		scrambled 	S08.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S09 	male 	26    6.00 	0.1767  56 		24 		words 		S09.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S09 	male 	26    6.00 	0.1767  56 		24 		scrambled 	S09.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S14 	male 	30    7.00 	0.0637  47 		35 		words 		S14.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S14 	male 	30    7.00 	0.0637  47 		35 		scrambled 	S14.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S12 	male 	24    4.75 	0.399   52 		34 		words 		S12.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S12 	male 	24    4.75 	0.399   52 		34 		scrambled 	S12.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S10 	female 	24    5.50 	0.1258  36 		32 		words 		S10.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S10 	female 	24    5.50 	0.1258  36 		32 		scrambled 	S10.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S11 	female 	25    5.00 	0.3598  36 		28 		words 		S11.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S11 	female 	25    5.00 	0.3598  36 		28 		scrambled 	S11.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S16 	female 	34    5.25 	0.1167  51 		31 		words 		S16.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S16 	female 	34    5.25 	0.1167  51 		31 		scrambled 	S16.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S13 	female 	30    7.25 	0.241   29 		39 		words 		S13.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S13 	female 	30    7.25 	0.241   29 		39 		scrambled 	S13.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S15 	male 	28    7.50 	0.0925  60 		51 		words 		S15.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S15 	male 	28    7.50 	0.0925  60 		51 		scrambled 	S15.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S17 	male 	26    7.25 	0.1849  38 		33 		words 		S17.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S17 	male 	26    7.25 	0.1849  38 		33 		scrambled 	S17.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S19 	female 	27    5.75 	0.1159  46 		31 		words 		S19.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S19 	female 	27    5.75 	0.1159  46 		31 		scrambled 	S19.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S18 	male 	25    4.75 	0.1808  50 		35 		words 		S18.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S18 	male 	25    4.75 	0.1808  50 		35 		scrambled 	S18.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S21 	female 	23    5.75 	0.153   42 		40 		words 		S21.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S21 	female 	23    5.75 	0.153   42 		40 		scrambled 	S21.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S20 	female 	27    6.50 	0.1276  45 		32 		words 		S20.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S20 	female 	27    6.50 	0.1276  45 		32 		scrambled 	S20.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S22 	female 	22    5.25 	0.1018  37 		29 		words 		S22.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S22 	female 	22    5.25 	0.1018  37 		29 		scrambled 	S22.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S23 	female 	26    6.00 	0.1453  46 		38 		words 		S23.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S23 	female 	26    6.00 	0.1453  46 		38 		scrambled 	S23.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S38 	female 	31    4.75 	0.092   68 		38 		words 		S38.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S38 	female 	31    4.75 	0.092   68 		38 		scrambled 	S38.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S24 	female 	21    5.25 	0.113   30 		20 		words 		S24.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S24 	female 	21    5.25 	0.113   30 		20 		scrambled 	S24.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S25 	female 	33    5.00 	0.1435  28 		19	 	words 		S25.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S25 	female 	33    5.00 	0.1435  28 		19	 	scrambled 	S25.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S27 	female 	27    7.25 	0.3087  44 		35 		words 		S27.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S27 	female 	27    7.25 	0.3087  44 		35 		scrambled 	S27.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S28 	female 	21    6.50 	0.3086  40 		26 		words 		S28.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S28 	female 	21    6.50 	0.3086  40 		26 		scrambled 	S28.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S31 	female 	23    4.25 	0.1218  17 		25	 	words 		S31.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S31 	female 	23    4.25 	0.1218  17 		25 		scrambled 	S31.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S34 	male 	27    6.00 	0.1976  54 		32 		words 		S34.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S34 	male 	27    6.00 	0.1976  54 		32 		scrambled 	S34.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S29 	female 	24    6.75 	0.1501  42 		28 		words 		S29.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S29 	female 	24    6.75 	0.1501  42 		28 		scrambled 	S29.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S26 	female 	21    6.75 	0.1446  46 		38 		words 		S26.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S26 	female 	21    6.75 	0.1446  46 		38 		scrambled 	S26.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S30 	female 	24    6.25 	0.1889  45 		27 		words 		S30.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S30 	female 	24    6.25 	0.1889  45 		27 		scrambled 	S30.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S43 	female 	20    6.00 	0.1816  39 		35 		words 		S43.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S43 	female 	20    6.00 	0.1816  39 		35 		scrambled 	S43.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S33 	male 	27    7.00 	0.1703  43 		27 		words 		S33.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S33 	male 	27    7.00 	0.1703  43 		27 		scrambled 	S33.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S32 	female 	30    6.75 	0.1353  37 		40 		words 		S32.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S32 	female 	30    6.75 	0.1353  37 		40 		scrambled 	S32.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S36 	male 	24    4.25 	0.1452  38 		27 		words 		S36.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S36 	male 	24    4.25 	0.1452  38 		27 		scrambled 	S36.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S35 	female 	21    5.25 	0.0276  32 		30 		words 		S35.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S35 	female 	21    5.25 	0.0276  32 		30 		scrambled 	S35.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S39 	female 	24    5.75 	0.067   59 		37 		words 		S39.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S39 	female 	24    5.75 	0.067   59 		37 		scrambled 	S39.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S37 	female 	23    5.75 	0.1906  34 		25 		words 		S37.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S37 	female 	23    5.75 	0.1906  34 		25 		scrambled 	S37.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S47 	male 	24    6.00 	0.1217  47 		29 		words 		S47.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S47 	male 	24    6.00 	0.1217  47 		29 		scrambled 	S47.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S40 	female 	27    6.50 	0.1938  36 		34 		words 		S40.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S40 	female 	27    6.50 	0.1938  36 		34 		scrambled 	S40.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S41 	female 	22    5.00 	0.237   45 		40 		words 		S41.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S41 	female 	22    5.00 	0.237   45 		40 		scrambled 	S41.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S45 	male 	30    7.00 	0.1566  60 		41 		words 		S45.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S45 	male 	30    7.00 	0.1566  60 		41 		scrambled 	S45.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S42 	female 	21    5.75 	0.1215  36 		30 		words 		S42.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S42 	female 	21    5.75 	0.1215  36 		30 		scrambled 	S42.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S44 	female 	31    6.75 	0.1588  57 		35 		words 		S44.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S44 	female 	31    6.75 	0.1588  57 		35 		scrambled 	S44.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]' \ 
S46 	female 	32    5.00 	0.191   40 		25 		words 		S46.single_subject_GLM_MNI+tlrc'[Words#0_Coef]' \ 
S46 	female 	32    5.00 	0.191   40 		25 		scrambled 	S46.single_subject_GLM_MNI+tlrc'[Scrambled#0_Coef]'

Is MVM still the right thing to do, even if I am interested in the covariate (i.e. Root_Fluency and Phon_Fluency),
while controlling for the categorical variable (Morph)?

It’s the variable types and data structure (not whether you’re interested a particular variable) that determine which program to use.

when trying to run 3dMVM I still get an error

What error did you get?

-wsVars Morph
-bsVars “Root_fluency+Phon_fluency”
-qVars “MIE,Root_fluency,Phon_fluency,WM,Age” \

You didn’t specify whether the variables “MIE”, “WM” and “Age” are between- or within-subject?

It is as if the "" in the end of each line is not recognized, so I get a lot of “Command not found” errors:


3dMVM -prefix MVM_GROUP_LEVEL_fluency2 -jobs 2 -wsVars Morph -bsVars Root_fluency+Phon_fluency -qVars Root_fluency,Phon_fluency -num_glt 2 -gltLabel 1 RootFluency_effect -gltCode 1 Morph : 1*words -1*scrambled Root_fluency : -gltLabel 2 PhonFluency_effect -gltCode 2 Morph : 1*words -1*scrambled Phon_fluency : -dataTable Subj Sex Age WM MIE Phon_fluency Root_fluency Morph InputFile  
Error in seq.default(wd + ii, len, wd) : wrong sign in 'by' argument
Calls: process.MVM.opts -> data.frame -> cbind -> seq -> seq.default
Execution halted
S05 male 30 7.25 0.226 49 29 words S05.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S05: Command not found.
S05 male 30 7.25 0.226 49 29 scrambled S05.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S05: Command not found.
S03 male 28 6.00 0.2248 37 29 words S03.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S03: Command not found.
S03 male 28 6.00 0.2248 37 29 scrambled S03.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S03: Command not found.
S04 male 34 6.00 0.3673 56 27 words S04.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S04: Command not found.
S04 male 34 6.00 0.3673 56 27 scrambled S04.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S04: Command not found.
S07 female 24 6.50 0.1125 41 21 words S07.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S07: Command not found.
S07 female 24 6.50 0.1125 41 21 scrambled S07.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S07: Command not found.
S08 male 24 6.75 0.119 47 24 words S08.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S08: Command not found.
S08 male 24 6.75 0.119 47 24 scrambled S08.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S08: Command not found.
S09 male 26 6.00 0.1767 56 24 words S09.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S09: Command not found.
S09 male 26 6.00 0.1767 56 24 scrambled S09.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S09: Command not found.
S14 male 30 7.00 0.0637 47 35 words S14.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S14: Command not found.
S14 male 30 7.00 0.0637 47 35 scrambled S14.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S14: Command not found.
S12 male 24 4.75 0.399 52 34 words S12.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S12: Command not found.
S12 male 24 4.75 0.399 52 34 scrambled S12.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S12: Command not found.
S10 female 24 5.50 0.1258 36 32 words S10.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S10: Command not found.
S10 female 24 5.50 0.1258 36 32 scrambled S10.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S10: Command not found.
S11 female 25 5.00 0.3598 36 28 words S11.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S11: Command not found.
S11 female 25 5.00 0.3598 36 28 scrambled S11.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S11: Command not found.
S16 female 34 5.25 0.1167 51 31 words S16.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S16: Command not found.
S16 female 34 5.25 0.1167 51 31 scrambled S16.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S16: Command not found.
S13 female 30 7.25 0.241 29 39 words S13.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S13: Command not found.
S13 female 30 7.25 0.241 29 39 scrambled S13.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S13: Command not found.
S15 male 28 7.50 0.0925 60 51 words S15.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S15: Command not found.
S15 male 28 7.50 0.0925 60 51 scrambled S15.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S15: Command not found.
S17 male 26 7.25 0.1849 38 33 words S17.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S17: Command not found.
S17 male 26 7.25 0.1849 38 33 scrambled S17.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S17: Command not found.
S19 female 27 5.75 0.1159 46 31 words S19.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S19: Command not found.
S19 female 27 5.75 0.1159 46 31 scrambled S19.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S19: Command not found.
S18 male 25 4.75 0.1808 50 35 words S18.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S18: Command not found.
S18 male 25 4.75 0.1808 50 35 scrambled S18.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S18: Command not found.
S21 female 23 5.75 0.153 42 40 words S21.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S21: Command not found.
S21 female 23 5.75 0.153 42 40 scrambled S21.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S21: Command not found.
S20 female 27 6.50 0.1276 45 32 words S20.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S20: Command not found.
S20 female 27 6.50 0.1276 45 32 scrambled S20.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S20: Command not found.
S22 female 22 5.25 0.1018 37 29 words S22.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S22: Command not found.
S22 female 22 5.25 0.1018 37 29 scrambled S22.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S22: Command not found.
S23 female 26 6.00 0.1453 46 38 words S23.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S23: Command not found.
S23 female 26 6.00 0.1453 46 38 scrambled S23.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S23: Command not found.
S38 female 31 4.75 0.092 68 38 words S38.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S38: Command not found.
S38 female 31 4.75 0.092 68 38 scrambled S38.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S38: Command not found.
S24 female 21 5.25 0.113 30 20 words S24.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S24: Command not found.
S24 female 21 5.25 0.113 30 20 scrambled S24.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S24: Command not found.
S25 female 33 5.00 0.1435 28 19 words S25.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S25: Command not found.
S25 female 33 5.00 0.1435 28 19 scrambled S25.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S25: Command not found.
S27 female 27 7.25 0.3087 44 35 words S27.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S27: Command not found.
S27 female 27 7.25 0.3087 44 35 scrambled S27.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S27: Command not found.
S28 female 21 6.50 0.3086 40 26 words S28.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S28: Command not found.
S28 female 21 6.50 0.3086 40 26 scrambled S28.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S28: Command not found.
S31 female 23 4.25 0.1218 17 25 words S31.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S31: Command not found.
S31 female 23 4.25 0.1218 17 25 scrambled S31.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S31: Command not found.
S34 male 27 6.00 0.1976 54 32 words S34.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S34: Command not found.
S34 male 27 6.00 0.1976 54 32 scrambled S34.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S34: Command not found.
S29 female 24 6.75 0.1501 42 28 words S29.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S29: Command not found.
S29 female 24 6.75 0.1501 42 28 scrambled S29.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S29: Command not found.
S26 female 21 6.75 0.1446 46 38 words S26.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S26: Command not found.
S26 female 21 6.75 0.1446 46 38 scrambled S26.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S26: Command not found.
S30 female 24 6.25 0.1889 45 27 words S30.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S30: Command not found.
S30 female 24 6.25 0.1889 45 27 scrambled S30.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S30: Command not found.
S43 female 20 6.00 0.1816 39 35 words S43.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S43: Command not found.
S43 female 20 6.00 0.1816 39 35 scrambled S43.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S43: Command not found.
S33 male 27 7.00 0.1703 43 27 words S33.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S33: Command not found.
S33 male 27 7.00 0.1703 43 27 scrambled S33.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S33: Command not found.
S32 female 30 6.75 0.1353 37 40 words S32.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S32: Command not found.
S32 female 30 6.75 0.1353 37 40 scrambled S32.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S32: Command not found.
S36 male 24 4.25 0.1452 38 27 words S36.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S36: Command not found.
S36 male 24 4.25 0.1452 38 27 scrambled S36.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S36: Command not found.
S35 female 21 5.25 0.0276 32 30 words S35.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S35: Command not found.
S35 female 21 5.25 0.0276 32 30 scrambled S35.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S35: Command not found.
S39 female 24 5.75 0.067 59 37 words S39.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S39: Command not found.
S39 female 24 5.75 0.067 59 37 scrambled S39.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S39: Command not found.
S37 female 23 5.75 0.1906 34 25 words S37.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S37: Command not found.
S37 female 23 5.75 0.1906 34 25 scrambled S37.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S37: Command not found.
S47 male 24 6.00 0.1217 47 29 words S47.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S47: Command not found.
S47 male 24 6.00 0.1217 47 29 scrambled S47.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S47: Command not found.
S40 female 27 6.50 0.1938 36 34 words S40.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S40: Command not found.
S40 female 27 6.50 0.1938 36 34 scrambled S40.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S40: Command not found.
S41 female 22 5.00 0.237 45 40 words S41.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S41: Command not found.
S41 female 22 5.00 0.237 45 40 scrambled S41.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S41: Command not found.
S45 male 30 7.00 0.1566 60 41 words S45.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S45: Command not found.
S45 male 30 7.00 0.1566 60 41 scrambled S45.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S45: Command not found.
S42 female 21 5.75 0.1215 36 30 words S42.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S42: Command not found.
S42 female 21 5.75 0.1215 36 30 scrambled S42.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S42: Command not found.
S44 female 31 6.75 0.1588 57 35 words S44.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S44: Command not found.
S44 female 31 6.75 0.1588 57 35 scrambled S44.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]  
S44: Command not found.
S46 female 32 5.00 0.191 40 25 words S46.single_subject_GLM_MNI+tlrc[Words#0_Coef]  
S46: Command not found.
S46 female 32 5.00 0.191 40 25 scrambled S46.single_subject_GLM_MNI+tlrc[Scrambled#0_Coef]
S46: Command not found.

I get it now with other commands as well, so I’m starting to think that it is not a problem with 3dMVM but some more general syntax problem.

Age was defined in qVars, but not in bsVars, becuase I decided I don’t want it in the model. I took it out of qVars as well - same result.

There is some empty space after one of the backslashes. Use the following command to find out the culprit:

file_tool -test -infiles your3dMVMscript

What an amazing command, thank you!!
It seems like it’s finally running now.

Hi,
I am a little late, but you could try the 3dMVM_validator to test your model and GLTs and it will create the 3dMVM script for you.
So you don’t have to worry about the extra spaces.
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/3dMVM_validator/3dMVM_validator_overview.html

thanks, Justin