3dMVM 2x2 failure

egarza · February 27, 2020, 10:17pm

Hi,

I’m trying to setup a Mixed Model with 1 between-subject factor (group: SHAM vs REAL) and 1 within-subjects factor (stage: T0 vs T1). The input files are all rsfMRI seed-based correlations converted to Z maps.

I keep getting Model Failure but I cannot find the mistake. Any help would be appreciated.

AFNI Version


afni -ver
Precompiled binary linux_ubuntu_16_64: Feb 24 2020 (Version AFNI_20.0.16 'Galba')

Call


bash mixedmodel_afni

Code


3dMVM -prefix TMSmixed_results -jobs 1 \
        -bsVars 'group' \
        -wsVars 'stage' \
        -mask /media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/data/normative_maps/rois/vmPFC_bin.nii.gz \
        -num_glt 5 \
        -gltLabel 1 interaction -gltCode 1 'group: 1*SHAM -1*REAL stage: 1*t1 -1*t0' \
        -gltLabel 2 sham_t0_vs_t1 -gltCode 2 'group: 1*SHAM stage: 1*t1 -1*t0' \
        -gltLabel 3 real_t0_vs_t1 -gltCode 3 'group: 1*REAL stage: 1*t1 -1*t0' \
        -gltLabel 4 t1-sham_vs_real -gltCode 4 'group: 1*SHAM -1*REAL stage: 1*t1' \
        -gltLabel 5 t0-sham_vs_real -gltCode 5 'group: 1*SHAM -1*REAL stage: 1*t0' \
        -dataTable @/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/dataTable.txt

dataTable


Subj	group	stage	InputFile  \
1	SHAM	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/1_ses-t0_stdlDLPFC_Z.nii.gz \
1	SHAM	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/1_ses-t1_stdlDLPFC_Z.nii.gz \
2	SHAM	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/2_ses-t0_stdlDLPFC_Z.nii.gz \
2	SHAM	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/2_ses-t1_stdlDLPFC_Z.nii.gz \
3	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/3_ses-t0_stdlDLPFC_Z.nii.gz \
3	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/3_ses-t1_stdlDLPFC_Z.nii.gz \
4	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/4_ses-t0_stdlDLPFC_Z.nii.gz \
4	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/4_ses-t1_stdlDLPFC_Z.nii.gz \
6	SHAM	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/6_ses-t0_stdlDLPFC_Z.nii.gz \
6	SHAM	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/6_ses-t1_stdlDLPFC_Z.nii.gz \
7	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/7_ses-t0_stdlDLPFC_Z.nii.gz \
7	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/7_ses-t1_stdlDLPFC_Z.nii.gz \
8	SHAM	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/8_ses-t0_stdlDLPFC_Z.nii.gz \
8	SHAM	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/8_ses-t1_stdlDLPFC_Z.nii.gz \
10	SHAM	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/10_ses-t0_stdlDLPFC_Z.nii.gz \
10	SHAM	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/10_ses-t1_stdlDLPFC_Z.nii.gz \
11	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/11_ses-t0_stdlDLPFC_Z.nii.gz \
11	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/11_ses-t1_stdlDLPFC_Z.nii.gz \
12	SHAM	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/12_ses-t0_stdlDLPFC_Z.nii.gz \
12	SHAM	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/12_ses-t1_stdlDLPFC_Z.nii.gz \
13	SHAM	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/13_ses-t0_stdlDLPFC_Z.nii.gz \
13	SHAM	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/13_ses-t1_stdlDLPFC_Z.nii.gz \
15	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/15_ses-t0_stdlDLPFC_Z.nii.gz \
15	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/15_ses-t1_stdlDLPFC_Z.nii.gz \
16	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/16_ses-t0_stdlDLPFC_Z.nii.gz \
16	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/16_ses-t1_stdlDLPFC_Z.nii.gz \
17	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/17_ses-t0_stdlDLPFC_Z.nii.gz \
17	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/17_ses-t1_stdlDLPFC_Z.nii.gz \
18	SHAM	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/18_ses-t0_stdlDLPFC_Z.nii.gz \
18	SHAM	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/18_ses-t1_stdlDLPFC_Z.nii.gz \
19	SHAM	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/19_ses-t0_stdlDLPFC_Z.nii.gz \
19	SHAM	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/19_ses-t1_stdlDLPFC_Z.nii.gz \
20	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/20_ses-t0_stdlDLPFC_Z.nii.gz \
20	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/20_ses-t1_stdlDLPFC_Z.nii.gz \
21	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/21_ses-t0_stdlDLPFC_Z.nii.gz \
21	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/21_ses-t1_stdlDLPFC_Z.nii.gz \
22	SHAM	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/22_ses-t0_stdlDLPFC_Z.nii.gz \
22	SHAM	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/22_ses-t1_stdlDLPFC_Z.nii.gz \
23	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/23_ses-t0_stdlDLPFC_Z.nii.gz \
23	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/23_ses-t1_stdlDLPFC_Z.nii.gz \
24	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/24_ses-t0_stdlDLPFC_Z.nii.gz \
24	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/24_ses-t1_stdlDLPFC_Z.nii.gz \
25	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/25_ses-t0_stdlDLPFC_Z.nii.gz \
25	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/25_ses-t1_stdlDLPFC_Z.nii.gz \
26	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/26_ses-t0_stdlDLPFC_Z.nii.gz \
26	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/26_ses-t1_stdlDLPFC_Z.nii.gz \
27	SHAM	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/27_ses-t0_stdlDLPFC_Z.nii.gz \
27	SHAM	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/27_ses-t1_stdlDLPFC_Z.nii.gz \
30	SHAM	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/30_ses-t0_stdlDLPFC_Z.nii.gz \
30	SHAM	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/30_ses-t1_stdlDLPFC_Z.nii.gz \
31	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/31_ses-t0_stdlDLPFC_Z.nii.gz \
31	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/31_ses-t1_stdlDLPFC_Z.nii.gz \
32	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/32_ses-t0_stdlDLPFC_Z.nii.gz \
32	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/32_ses-t1_stdlDLPFC_Z.nii.gz \
33	SHAM	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/33_ses-t0_stdlDLPFC_Z.nii.gz \
33	SHAM	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/33_ses-t1_stdlDLPFC_Z.nii.gz \
34	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/34_ses-t0_stdlDLPFC_Z.nii.gz \
34	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/34_ses-t1_stdlDLPFC_Z.nii.gz \
36	SHAM	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/36_ses-t0_stdlDLPFC_Z.nii.gz \
36	SHAM	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/36_ses-t1_stdlDLPFC_Z.nii.gz \
37	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/37_ses-t0_stdlDLPFC_Z.nii.gz \
37	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/37_ses-t1_stdlDLPFC_Z.nii.gz \
39	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/39_ses-t0_stdlDLPFC_Z.nii.gz \
39	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/39_ses-t1_stdlDLPFC_Z.nii.gz \
41	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/41_ses-t0_stdlDLPFC_Z.nii.gz \
41	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/41_ses-t1_stdlDLPFC_Z.nii.gz \
42	SHAM	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/42_ses-t0_stdlDLPFC_Z.nii.gz \
42	SHAM	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/42_ses-t1_stdlDLPFC_Z.nii.gz \
43	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/43_ses-t0_stdlDLPFC_Z.nii.gz \
43	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/43_ses-t1_stdlDLPFC_Z.nii.gz \
45	SHAM	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/45_ses-t0_stdlDLPFC_Z.nii.gz \
45	SHAM	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/45_ses-t1_stdlDLPFC_Z.nii.gz \
46	SHAM	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/46_ses-t0_stdlDLPFC_Z.nii.gz \
46	SHAM	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/46_ses-t1_stdlDLPFC_Z.nii.gz \
47	SHAM	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/47_ses-t0_stdlDLPFC_Z.nii.gz \
47	SHAM	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/47_ses-t1_stdlDLPFC_Z.nii.gz \
48	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/48_ses-t0_stdlDLPFC_Z.nii.gz \
48	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/48_ses-t1_stdlDLPFC_Z.nii.gz \
49	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/49_ses-t0_stdlDLPFC_Z.nii.gz \
49	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/49_ses-t1_stdlDLPFC_Z.nii.gz \
50	SHAM	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/50_ses-t0_stdlDLPFC_Z.nii.gz \
50	SHAM	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/50_ses-t1_stdlDLPFC_Z.nii.gz \
52	SHAM	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/52_ses-t0_stdlDLPFC_Z.nii.gz \
52	SHAM	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/52_ses-t1_stdlDLPFC_Z.nii.gz \
53	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/53_ses-t0_stdlDLPFC_Z.nii.gz \
53	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/53_ses-t1_stdlDLPFC_Z.nii.gz \
54	REAL	t0	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/54_ses-t0_stdlDLPFC_Z.nii.gz \
54	REAL	t1	/media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/analysis/AFNI/Zmaps/54_ses-t1_stdlDLPFC_Z.nii.gz \

Error msg


Read 443 items
Loading required package: lme4
Loading required package: Matrix
Registered S3 methods overwritten by 'car':
  method                          from
  influence.merMod                lme4
  cooks.distance.influence.merMod lme4
  dfbeta.influence.merMod         lme4
  dfbetas.influence.merMod        lme4
************
Welcome to afex. For support visit: http://afex.singmann.science/
- Functions for ANOVAs: aov_car(), aov_ez(), and aov_4()
- Methods for calculating p-values with mixed(): 'KR', 'S', 'LRT', and 'PB'
- 'afex_aov' and 'mixed' objects can be passed to emmeans() for follow-up tests
- NEWS: library('emmeans') now needs to be called explicitly!
- Get and set global package options with: afex_options()
- Set orthogonal sum-to-zero contrasts globally: set_sum_contrasts()
- For example analyses see: browseVignettes("afex")
************

Attaching package: ‘afex’

The following object is masked from ‘package:lme4’:

    lmer

Loading required package: car
Loading required package: carData

++++++++++++++++++++++++++++++++++++++++++++++++++++
***** Summary information of data structure *****
44 subjects :  1 10 11 12 13 15 16 17 18 19 2 20 21 22 23 24 25 26 27 3 30 31 32 33 34 36 37 39 4 41 42 43 45 46 47 48 49 50 52 53 54 6 7 8 
88 response values
2 levels for factor group : REAL SHAM 
2 levels for factor stage : t0 t1 
5 post hoc tests

Contingency tables of subject distributions among the categorical variables:

      stage
group  t0 t1
  REAL 24 24
  SHAM 20 20

Tabulation of subjects against each of the categorical variables:
~~~~~~~~~~~~~~
lop$nSubj vs group:
    
     REAL SHAM
  1     0    2
  10    0    2
  11    2    0
  12    0    2
  13    0    2
  15    2    0
  16    2    0
  17    2    0
  18    0    2
  19    0    2
  2     0    2
  20    2    0
  21    2    0
  22    0    2
  23    2    0
  24    2    0
  25    2    0
  26    2    0
  27    0    2
  3     2    0
  30    0    2
  31    2    0
  32    2    0
  33    0    2
  34    2    0
  36    0    2
  37    2    0
  39    2    0
  4     2    0
  41    2    0
  42    0    2
  43    2    0
  45    0    2
  46    0    2
  47    0    2
  48    2    0
  49    2    0
  50    0    2
  52    0    2
  53    2    0
  54    2    0
  6     0    2
  7     2    0
  8     0    2

~~~~~~~~~~~~~~
lop$nSubj vs stage:
    
     t0 t1
  1   1  1
  10  1  1
  11  1  1
  12  1  1
  13  1  1
  15  1  1
  16  1  1
  17  1  1
  18  1  1
  19  1  1
  2   1  1
  20  1  1
  21  1  1
  22  1  1
  23  1  1
  24  1  1
  25  1  1
  26  1  1
  27  1  1
  3   1  1
  30  1  1
  31  1  1
  32  1  1
  33  1  1
  34  1  1
  36  1  1
  37  1  1
  39  1  1
  4   1  1
  41  1  1
  42  1  1
  43  1  1
  45  1  1
  46  1  1
  47  1  1
  48  1  1
  49  1  1
  50  1  1
  52  1  1
  53  1  1
  54  1  1
  6   1  1
  7   1  1
  8   1  1

***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++

Reading input files now...

Reading input files: Done!

If the program hangs here for more than, for example, half an hour,
kill the process because the model specification or the GLT coding
is likely inappropriate.

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

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

1) Inappropriate model specification with options -bsVars, -wsVars, or -qVars.
Note that within-subject or repeated-measures variables have to be declared
with -wsVars.

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 3dMVM.

5) Not enough number of subjects. This may happen when there are two or more
withi-subject factors. For example, a model with two within-subject factors with
m and n levels respectively requires more than (m-1)*(n-1) subjects to be able to
model the two-way interaction with the multivariate approach.


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

Gang · February 28, 2020, 1:40am

Try changing the following

    -gltLabel 1 interaction -gltCode 1 'group: 1*SHAM -1*REAL stage: 1*t1 -1*t0' \
    -gltLabel 2 sham_t0_vs_t1 -gltCode 2 'group: 1*SHAM stage: 1*t1 -1*t0' \
    -gltLabel 3 real_t0_vs_t1 -gltCode 3 'group: 1*REAL stage: 1*t1 -1*t0' \
    -gltLabel 4 t1-sham_vs_real -gltCode 4 'group: 1*SHAM -1*REAL stage: 1*t1' \
    -gltLabel 5 t0-sham_vs_real -gltCode 5 'group: 1*SHAM -1*REAL stage: 1*t0' \

to (adding a space before each colon)

    -gltLabel 1 interaction -gltCode 1 'group : 1*SHAM -1*REAL stage : 1*t1 -1*t0' \
    -gltLabel 2 sham_t0_vs_t1 -gltCode 2 'group : 1*SHAM stage : 1*t1 -1*t0' \
    -gltLabel 3 real_t0_vs_t1 -gltCode 3 'group : 1*REAL stage : 1*t1 -1*t0' \
    -gltLabel 4 t1-sham_vs_real -gltCode 4 'group : 1*SHAM -1*REAL stage : 1*t1' \
    -gltLabel 5 t0-sham_vs_real -gltCode 5 'group : 1*SHAM -1*REAL stage : 1*t0' \

egarza · February 28, 2020, 3:14pm

It didn’t work.

The dataTable is TAB separated, may that be an issue?

I can’t tell what else may be wrong.

Gang · February 28, 2020, 5:42pm

Those 5 lines for post hoc inferences in the original script were definitely problematic. Now, the mask could be an issue. Remove the following line, and run the script. You can apply the mask after the analysis.

-mask /media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/data/normative_maps/rois/vmPFC_bin.nii.gz \

egarza · February 28, 2020, 6:28pm

Great, the mask was the problem. It’s now running. Will report if anything fails.

How can I add it later? I’m new to AFNI and I have a prior hypothesis.

Thanks!

Eduardo

Gang · February 28, 2020, 7:09pm

You can apply the mask on your 3dMVM output as follows:

3dcalc -a my3dMVMoutput -b /media/egarza/Elements2/projects/ADDIMEX_TMS/FC_CLIN/3-Experiment/data/normative_maps/rois/vmPFC_bin.nii.gz -expr ‘a*b’ -prefix myMaskedResult

In your 3dMVM, you specified the output file as “3dMVM -prefix TMSmixed_results” which will give you an output in AFNI format. If you prefer an NIfTI output, you can convert the file in ANFI format through

3dcopy TMSmixed_results… TMSmixed_results.nii

In the future, to directly get the output in NIfTI format, do this:

3dMVM -prefix TMSmixed_results.nii …

egarza · February 28, 2020, 7:57pm

Thanks, I’ll try this and get back to you.