Error: $ operator is invalid for atomic vectors

MikeyMalina · June 1, 2022, 6:49pm

Hello,

I’ve received an error when attempting to run a 3x2 ANOVA through 3dMVM. I have never seen this error before, it seems to be R-related. Any ideas on solutions or better ways of structuring the ANOVA. The file was run with more than enough memory. My runfile code is below, and in the actual .txt file the columns are separated appropriately.

Thank you,
Mikey


3dMVM -prefix ST_ANOVA_aVf_HCvPCvIED -jobs 64 \
-bsVars 'condition*age+sex' \
-wsVars 'contrasts'\
-qVars 'age,motion' \
-qVarCenters '31.557,0.07949' \
-num_glf 1 \
-glfLabel 1 ST_ANOVA_aVf_HCvPCvIED -glfCode 1 'contrasts : 1*angry -1*fear condition : 1*HC -1*IED & 1*HC -1*PC & 1*IED -1*PC'\
-dataTable \
Subj	condition	age	sex	motion	contrasts	InputFile \
1	HC		45	1	0.08807	angry		stats.001_REML+tlrc.'[20]'\
6	HC		26	2	0.0640	angry		stats.006_REML+tlrc.'[20]'\
8	HC		33	1	0.0884	angry		stats.008_REML+tlrc.'[20]'\
9	HC		49	1	0.0657	angry		stats.009_REML+tlrc.'[20]'\
10	HC		25	2	0.0337	angry		stats.010_REML+tlrc.'[20]'\
20	HC		33	2	0.0532	angry		stats.020_REML+tlrc.'[20]'\
21	HC		37	2	0.0663	angry		stats.021_REML+tlrc.'[20]'\
23	HC		49	2	0.0768	angry		stats.023_REML+tlrc.'[20]'\
27	HC		31	2	0.0569	angry		stats.027_REML+tlrc.'[20]'\
31	HC		27	2	0.0548	angry		stats.031_REML+tlrc.'[20]'\
36	HC		23	2	0.0716	angry		stats.036_REML+tlrc.'[20]'\
45	HC		46	2	0.0990	angry		stats.045_REML+tlrc.'[20]'\
47	HC		23	2	0.0420	angry		stats.047_REML+tlrc.'[20]'\
50	HC		21	1	0.1000	angry		stats.050_REML+tlrc.'[20]'\
52	HC		22	1	0.0453	angry		stats.052_REML+tlrc.'[20]'\
55	HC		54	2	0.1110	angry		stats.055_REML+tlrc.'[20]'\
57	HC		23	1	0.0318	angry		stats.057_REML+tlrc.'[20]'\
58	HC		24	2	0.0534	angry		stats.058_REML+tlrc.'[20]'\
60	HC		21	2	0.0289	angry		stats.060_REML+tlrc.'[20]'\
61	HC		48	1	0.0438	angry		stats.061_REML+tlrc.'[20]'\
64	HC		26	2	0.1040	angry		stats.064_REML+tlrc.'[20]'\
66	HC		29	1	0.0300	angry		stats.066_REML+tlrc.'[20]'\
70	HC		22	1	0.0564	angry		stats.070_REML+tlrc.'[20]'\
71	HC		27	2	0.0381	angry		stats.071_REML+tlrc.'[20]'\
78	HC		21	2	0.0396	angry		stats.078_REML+tlrc.'[20]'\
14	IED		39	1	0.0323	angry		stats.014_REML+tlrc.'[20]'\
16	IED		21	1	0.047	angry		stats.016_REML+tlrc.'[20]'\
17	IED		51	1	0.0546	angry		stats.017_REML+tlrc.'[20]'\
19	IED		44	1	0.0776	angry		stats.019_REML+tlrc.'[20]'\
29	IED		25	1	0.0555	angry		stats.029_REML+tlrc.'[20]'\
34	IED		53	2	0.043	angry		stats.034_REML+tlrc.'[20]'\
39	IED		26	1	0.0676	angry		stats.039_REML+tlrc.'[20]'\
40	IED		27	1	0.0659	angry		stats.040_REML+tlrc.'[20]'\
41	IED		32	1	0.046	angry		stats.041_REML+tlrc.'[20]'\
46	IED		37	2	0.0409	angry		stats.046_REML+tlrc.'[20]'\
56	IED		47	1	0.0498	angry		stats.056_REML+tlrc.'[20]'\
67	IED		48	1	0.0554	angry		stats.067_REML+tlrc.'[20]'\
79	IED		28	2	0.0325	angry		stats.079_REML+tlrc.'[20]'\
80	IED		28	2	0.0415	angry		stats.080_REML+tlrc.'[20]'\
81	IED		37	2	0.0826	angry		stats.081_REML+tlrc.'[20]'\
83	IED		33	2	0.125	angry		stats.083_REML+tlrc.'[20]'\
84	IED		25	2	0.0634	angry		stats.084_REML+tlrc.'[20]'\
87	IED		38	1	0.087	angry		stats.087_REML+tlrc.'[20]'\
88	IED		31	1	0.06	angry		stats.088_REML+tlrc.'[20]'\
90	IED		31	1	0.0563	angry		stats.090_REML+tlrc.'[20]'\
91	IED		26	1	0.101	angry		stats.091_REML+tlrc.'[20]'\
4	PC		21	2	0.0341	angry		stats.004_REML+tlrc.'[20]'\
7	PC		28	1	0.045	angry		stats.007_REML+tlrc.'[20]'\
11	PC		25	1	0.0269	angry		stats.011_REML+tlrc.'[20]'\
12	PC		36	1	0.154	angry		stats.012_REML+tlrc.'[20]'\
13	PC		22	1	0.029	angry		stats.013_REML+tlrc.'[20]'\
15	PC		43	1	0.0368	angry		stats.015_REML+tlrc.'[20]'\
18	PC		48	1	0.0305	angry		stats.018_REML+tlrc.'[20]'\
22	PC		23	1	0.044	angry		stats.022_REML+tlrc.'[20]'\
24	PC		23	2	0.045	angry		stats.024_REML+tlrc.'[20]'\
25	PC		24	2	0.0359	angry		stats.025_REML+tlrc.'[20]'\
26	PC		28	2	0.0505	angry		stats.026_REML+tlrc.'[20]'\
28	PC		27	2	0.042	angry		stats.028_REML+tlrc.'[20]'\
30	PC		24	1	0.0369	angry		stats.030_REML+tlrc.'[20]'\
33	PC		22	1	0.0524	angry		stats.033_REML+tlrc.'[20]'\
35	PC		25	2	0.0793	angry		stats.035_REML+tlrc.'[20]'\
38	PC		21	2	0.108	angry		stats.038_REML+tlrc.'[20]'\
43	PC		30	1	0.0449	angry		stats.043_REML+tlrc.'[20]'\
48	PC		33	2	0.0335	angry		stats.048_REML+tlrc.'[20]'\
51	PC		23	2	0.0365	angry		stats.051_REML+tlrc.'[20]'\
53	PC		30	1	0.0502	angry		stats.053_REML+tlrc.'[20]'\
59	PC		22	2	0.1047	angry		stats.059_REML+tlrc.'[20]'\
63	PC		28	2	0.0545	angry		stats.063_REML+tlrc.'[20]'\
72	PC		40	2	0.0339	angry		stats.072_REML+tlrc.'[20]'\
74	PC		23	1	0.0398	angry		stats.074_REML+tlrc.'[20]'\
75	PC		43	1	0.0433	angry		stats.075_REML+tlrc.'[20]'\
86	PC		35	1	0.0784	angry		stats.086_REML+tlrc.'[20]'\
1	HC		45	1	0.08807	fear		stats.001_REML+tlrc.'[23]'\
6	HC		26	2	0.0640	fear		stats.006_REML+tlrc.'[23]'\
8	HC		33	1	0.0884	fear		stats.008_REML+tlrc.'[23]'\
9	HC		49	1	0.0657	fear		stats.009_REML+tlrc.'[23]'\
10	HC		25	2	0.0337	fear		stats.010_REML+tlrc.'[23]'\
20	HC		33	2	0.0532	fear		stats.020_REML+tlrc.'[23]'\
21	HC		37	2	0.0663	fear		stats.021_REML+tlrc.'[23]'\
23	HC		49	2	0.0768	fear		stats.023_REML+tlrc.'[23]'\
27	HC		31	2	0.0569	fear		stats.027_REML+tlrc.'[23]'\
31	HC		27	2	0.0548	fear		stats.031_REML+tlrc.'[23]'\
36	HC		23	2	0.0716	fear		stats.036_REML+tlrc.'[23]'\
45	HC		46	2	0.0990	fear		stats.045_REML+tlrc.'[23]'\
47	HC		23	2	0.0420	fear		stats.047_REML+tlrc.'[23]'\
50	HC		21	1	0.1000	fear		stats.050_REML+tlrc.'[23]'\
52	HC		22	1	0.0453	fear		stats.052_REML+tlrc.'[23]'\
55	HC		54	2	0.1110	fear		stats.055_REML+tlrc.'[23]'\
57	HC		23	1	0.0318	fear		stats.057_REML+tlrc.'[23]'\
58	HC		24	2	0.0534	fear		stats.058_REML+tlrc.'[23]'\
60	HC		21	2	0.0289	fear		stats.060_REML+tlrc.'[23]'\
61	HC		48	1	0.0438	fear		stats.061_REML+tlrc.'[23]'\
64	HC		26	2	0.1040	fear		stats.064_REML+tlrc.'[23]'\
66	HC		29	1	0.0300	fear		stats.066_REML+tlrc.'[23]'\
70	HC		22	1	0.0564	fear		stats.070_REML+tlrc.'[23]'\
71	HC		27	2	0.0381	fear		stats.071_REML+tlrc.'[23]'\
78	HC		21	2	0.0396	fear		stats.078_REML+tlrc.'[23]'\
14	IED		39	1	0.0323	fear		stats.014_REML+tlrc.'[23]'\
16	IED		21	1	0.047	fear		stats.016_REML+tlrc.'[23]'\
17	IED		51	1	0.0546	fear		stats.017_REML+tlrc.'[23]'\
19	IED		44	1	0.0776	fear		stats.019_REML+tlrc.'[23]'\
29	IED		25	1	0.0555	fear		stats.029_REML+tlrc.'[23]'\
34	IED		53	2	0.043	fear		stats.034_REML+tlrc.'[23]'\
39	IED		26	1	0.0676	fear		stats.039_REML+tlrc.'[23]'\
40	IED		27	1	0.0659	fear		stats.040_REML+tlrc.'[23]'\
41	IED		32	1	0.046	fear		stats.041_REML+tlrc.'[23]'\
46	IED		37	2	0.0409	fear		stats.046_REML+tlrc.'[23]'\
56	IED		47	1	0.0498	fear		stats.056_REML+tlrc.'[23]'\
67	IED		48	1	0.0554	fear		stats.067_REML+tlrc.'[23]'\
79	IED		28	2	0.0325	fear		stats.079_REML+tlrc.'[23]'\
80	IED		28	2	0.0415	fear		stats.080_REML+tlrc.'[23]'\
81	IED		37	2	0.0826	fear		stats.081_REML+tlrc.'[23]'\
83	IED		33	2	0.125	fear		stats.083_REML+tlrc.'[23]'\
84	IED		25	2	0.0634	fear		stats.084_REML+tlrc.'[23]'\
87	IED		38	1	0.087	fear		stats.087_REML+tlrc.'[23]'\
88	IED		31	1	0.06	fear		stats.088_REML+tlrc.'[23]'\
90	IED		31	1	0.0563	fear		stats.090_REML+tlrc.'[23]'\
91	IED		26	1	0.101	fear		stats.091_REML+tlrc.'[23]'\
4	PC		21	2	0.0341	fear		stats.004_REML+tlrc.'[23]'\
7	PC		28	1	0.045	fear		stats.007_REML+tlrc.'[23]'\
11	PC		25	1	0.0269	fear		stats.011_REML+tlrc.'[23]'\
12	PC		36	1	0.154	fear		stats.012_REML+tlrc.'[23]'\
13	PC		22	1	0.029	fear		stats.013_REML+tlrc.'[23]'\
15	PC		43	1	0.0368	fear		stats.015_REML+tlrc.'[23]'\
18	PC		48	1	0.0305	fear		stats.018_REML+tlrc.'[23]'\
22	PC		23	1	0.044	fear		stats.022_REML+tlrc.'[23]'\
24	PC		23	2	0.045	fear		stats.024_REML+tlrc.'[23]'\
25	PC		24	2	0.0359	fear		stats.025_REML+tlrc.'[23]'\
26	PC		28	2	0.0505	fear		stats.026_REML+tlrc.'[23]'\
28	PC		27	2	0.042	fear		stats.028_REML+tlrc.'[23]'\
30	PC		24	1	0.0369	fear		stats.030_REML+tlrc.'[23]'\
33	PC		22	1	0.0524	fear		stats.033_REML+tlrc.'[23]'\
35	PC		25	2	0.0793	fear		stats.035_REML+tlrc.'[23]'\
38	PC		21	2	0.108	fear		stats.038_REML+tlrc.'[23]'\
43	PC		30	1	0.0449	fear		stats.043_REML+tlrc.'[23]'\
48	PC		33	2	0.0335	fear		stats.048_REML+tlrc.'[23]'\
51	PC		23	2	0.0365	fear		stats.051_REML+tlrc.'[23]'\
53	PC		30	1	0.0502	fear		stats.053_REML+tlrc.'[23]'\
59	PC		22	2	0.1047	fear		stats.059_REML+tlrc.'[23]'\
63	PC		28	2	0.0545	fear		stats.063_REML+tlrc.'[23]'\
72	PC		40	2	0.0339	fear		stats.072_REML+tlrc.'[23]'\
74	PC		23	1	0.0398	fear		stats.074_REML+tlrc.'[23]'\
75	PC		43	1	0.0433	fear		stats.075_REML+tlrc.'[23]'\
86	PC		35	1	0.0784	fear		stats.086_REML+tlrc.'[23]'\

Gang · June 2, 2022, 5:29pm

-bsVars ‘condition*age+sex’
-wsVars ‘contrasts’
-qVars ‘age,motion’ \

You didn’t specify the variable ‘motion’ in the first two lines above. Maybe try the following

-bsVars ‘condition*age+sex+motion’
-wsVars ‘contrasts’
-qVars ‘age,motion’ \

MikeyMalina · June 2, 2022, 8:41pm

Hey Gang, thanks for the quick response.

Unfortunately, that did not solve the problem. I get the same error message following update of my bsVar line.

Thanks,
Mikey

Gang · June 5, 2022, 6:15pm

3dMVM validator may help diagnose the problem:

https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/3dMVM_validator/main_toc.htmlhttps://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/3dMVM_validator/main_toc.html

-glfLabel 1 ST_ANOVA_aVf_HCvPCvIED -glfCode 1 ‘contrasts : 1angry -1fear condition : 1HC -1IED & 1HC -1PC & 1IED -1PC’\

This specification does not make sense. By default 3dMVM would automatically provide the interaction assessment for this interaction between “condition” and “contrasts”. Nevertheless, with three conditions, the specification should be something like

-glfCode 1 ‘contrasts : 1angry -1fear condition : 1HC -1IED & 1HC -1PC’\