Hello,
We receive an error when running a 3dMVM script. Below are the script output, script code, and AFNI system check output. Can you please help troubleshoot?
Thanks,
Eddie
Script output:
[eazuniga1@carimri-ws3 scripts]$ ./5n2_groupmap-maker-Nback-multi-group
Checking dataTable file:
3dMVM-DataTable-NBack.txt
++Good: Table is regular and rectangular.
Read 5284 items
Dimensions:
rows: 880 | columns: 5
Data summary:
Variable Detected_Type Details
Subj Subjects Num Subjects=110
group Categorical Unique levels=4
mem_demand Categorical Counts: 0-back=440 | 2-back=440
stimulus Categorical Unique levels=4
InputFile Data Number of InputFiles=880
++ Good: All InputFiles exist.
++ Good: All InputFiles have exactly 1 volume.
++ Good: All InputFiles are on the same grid.
Loading required package: lme4
Loading required package: Matrix
************
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(): 'S', 'KR', 'LRT', and 'PB'
- 'afex_aov' and 'mixed' objects can be passed to emmeans() for follow-up tests
- Get and set global package options with: afex_options()
- Set 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 *****
110 subjects : VCU1001 VCU1002 VCU1003 VCU1004 VCU1005 VCU1007 VCU1008 VCU1009 VCU1010 VCU1011 VCU1012 VCU1013 VCU1014 VCU1017 VCU1019 VCU1020 VCU1021 VCU1022 VCU1024 VCU1025 VCU1026 VCU1027 VCU1028 VCU1029 VCU1030 VCU1031 VCU1032 VCU1033 VCU1036 VCU1037 VCU1038 VCU1039 VCU1040 VCU1041 VCU1042 VCU1043 VCU1044 VCU1045 VCU1046 VCU1047 VCU1048 VCU1049 VCU1050 VCU1051 VCU1054 VCU1055 VCU1056 VCU1057 VCU1058 VCU1059 VCU1060 VCU1061 VCU1062 VCU1063 VCU1065 VCU1066 VCU1067 VCU1068 VCU1069 VCU1070 VCU1071 VCU1072 VCU1073 VCU1074 VCU1075 VCU1076 VCU1077 VCU1078 VCU1079 VCU1080 VCU1082 VCU1083 VCU1084 VCU1085 VCU1086 VCU1087 VCU1088 VCU1089 VCU1090 VCU1091 VCU1094 VCU1095 VCU1096 VCU1098 VCU1099 VCU1101 VCU1102 VCU1105 VCU1106 VCU1107 VCU1108 VCU1109 VCU1110 VCU1112 VCU1113 VCU1114 VCU1115 VCU1117 VCU1118 VCU1120 VCU1121 VCU1122 VCU1123 VCU1124 VCU1126 VCU1128 VCU1129 VCU1130 VCU1131 VCU1134
880 response values
4 levels for factor group : amph control heroin poly
2 levels for factor mem_demand : 0-back 2-back
4 levels for factor stimulus : fear neu place pos
24 post hoc tests
Contingency tables of subject distributions among the categorical variables:
, , stimulus = fear
mem_demand
group 0-back 2-back
amph 37 37
control 28 28
heroin 28 28
poly 17 17
, , stimulus = neu
mem_demand
group 0-back 2-back
amph 37 37
control 28 28
heroin 28 28
poly 17 17
, , stimulus = place
mem_demand
group 0-back 2-back
amph 37 37
control 28 28
heroin 28 28
poly 17 17
, , stimulus = pos
mem_demand
group 0-back 2-back
amph 37 37
control 28 28
heroin 28 28
poly 17 17
Tabulation of subjects against each of the categorical variables:
~~~~~~~~~~~~~~
lop$nSubj vs group:
amph control heroin poly
VCU1001 0 8 0 0
VCU1002 0 0 8 0
VCU1003 8 0 0 0
VCU1004 0 0 8 0
VCU1005 8 0 0 0
VCU1007 0 8 0 0
VCU1008 0 0 8 0
VCU1009 0 8 0 0
VCU1010 0 0 8 0
VCU1011 0 0 8 0
VCU1012 8 0 0 0
VCU1013 0 0 8 0
VCU1014 0 0 8 0
VCU1017 0 0 8 0
VCU1019 0 8 0 0
VCU1020 0 8 0 0
VCU1021 0 8 0 0
VCU1022 0 0 8 0
VCU1024 0 8 0 0
VCU1025 0 8 0 0
VCU1026 0 0 8 0
VCU1027 0 8 0 0
VCU1028 0 8 0 0
VCU1029 0 0 8 0
VCU1030 8 0 0 0
VCU1031 0 8 0 0
VCU1032 0 8 0 0
VCU1033 8 0 0 0
VCU1036 0 0 8 0
VCU1037 0 0 8 0
VCU1038 0 8 0 0
VCU1039 0 0 8 0
VCU1040 0 8 0 0
VCU1041 8 0 0 0
VCU1042 8 0 0 0
VCU1043 0 8 0 0
VCU1044 0 8 0 0
VCU1045 0 8 0 0
VCU1046 0 0 8 0
VCU1047 0 0 8 0
VCU1048 8 0 0 0
VCU1049 8 0 0 0
VCU1050 8 0 0 0
VCU1051 0 0 8 0
VCU1054 0 8 0 0
VCU1055 0 8 0 0
VCU1056 0 8 0 0
VCU1057 0 0 0 8
VCU1058 8 0 0 0
VCU1059 0 0 0 8
VCU1060 0 0 8 0
VCU1061 0 0 8 0
VCU1062 0 8 0 0
VCU1063 8 0 0 0
VCU1065 8 0 0 0
VCU1066 8 0 0 0
VCU1067 8 0 0 0
VCU1068 0 0 0 8
VCU1069 0 0 0 8
VCU1070 0 8 0 0
VCU1071 8 0 0 0
VCU1072 8 0 0 0
VCU1073 0 0 0 8
VCU1074 0 0 0 8
VCU1075 8 0 0 0
VCU1076 8 0 0 0
VCU1077 0 0 8 0
VCU1078 0 0 8 0
VCU1079 0 0 0 8
VCU1080 8 0 0 0
VCU1082 8 0 0 0
VCU1083 0 0 8 0
VCU1084 8 0 0 0
VCU1085 0 0 8 0
VCU1086 0 0 0 8
VCU1087 0 0 8 0
VCU1088 0 0 0 8
VCU1089 8 0 0 0
VCU1090 0 0 0 8
VCU1091 0 0 0 8
VCU1094 0 8 0 0
VCU1095 8 0 0 0
VCU1096 8 0 0 0
VCU1098 8 0 0 0
VCU1099 8 0 0 0
VCU1101 0 0 8 0
VCU1102 0 0 8 0
VCU1105 8 0 0 0
VCU1106 8 0 0 0
VCU1107 0 0 0 8
VCU1108 8 0 0 0
VCU1109 0 8 0 0
VCU1110 0 8 0 0
VCU1112 0 0 0 8
VCU1113 0 8 0 0
VCU1114 0 0 8 0
VCU1115 0 0 8 0
VCU1117 8 0 0 0
VCU1118 8 0 0 0
VCU1120 0 0 0 8
VCU1121 0 0 0 8
VCU1122 0 0 0 8
VCU1123 8 0 0 0
VCU1124 0 8 0 0
VCU1126 8 0 0 0
VCU1128 0 0 0 8
VCU1129 8 0 0 0
VCU1130 8 0 0 0
VCU1131 8 0 0 0
VCU1134 0 8 0 0
~~~~~~~~~~~~~~
lop$nSubj vs mem_demand:
0-back 2-back
VCU1001 4 4
VCU1002 4 4
VCU1003 4 4
VCU1004 4 4
VCU1005 4 4
VCU1007 4 4
VCU1008 4 4
VCU1009 4 4
VCU1010 4 4
VCU1011 4 4
VCU1012 4 4
VCU1013 4 4
VCU1014 4 4
VCU1017 4 4
VCU1019 4 4
VCU1020 4 4
VCU1021 4 4
VCU1022 4 4
VCU1024 4 4
VCU1025 4 4
VCU1026 4 4
VCU1027 4 4
VCU1028 4 4
VCU1029 4 4
VCU1030 4 4
VCU1031 4 4
VCU1032 4 4
VCU1033 4 4
VCU1036 4 4
VCU1037 4 4
VCU1038 4 4
VCU1039 4 4
VCU1040 4 4
VCU1041 4 4
VCU1042 4 4
VCU1043 4 4
VCU1044 4 4
VCU1045 4 4
VCU1046 4 4
VCU1047 4 4
VCU1048 4 4
VCU1049 4 4
VCU1050 4 4
VCU1051 4 4
VCU1054 4 4
VCU1055 4 4
VCU1056 4 4
VCU1057 4 4
VCU1058 4 4
VCU1059 4 4
VCU1060 4 4
VCU1061 4 4
VCU1062 4 4
VCU1063 4 4
VCU1065 4 4
VCU1066 4 4
VCU1067 4 4
VCU1068 4 4
VCU1069 4 4
VCU1070 4 4
VCU1071 4 4
VCU1072 4 4
VCU1073 4 4
VCU1074 4 4
VCU1075 4 4
VCU1076 4 4
VCU1077 4 4
VCU1078 4 4
VCU1079 4 4
VCU1080 4 4
VCU1082 4 4
VCU1083 4 4
VCU1084 4 4
VCU1085 4 4
VCU1086 4 4
VCU1087 4 4
VCU1088 4 4
VCU1089 4 4
VCU1090 4 4
VCU1091 4 4
VCU1094 4 4
VCU1095 4 4
VCU1096 4 4
VCU1098 4 4
VCU1099 4 4
VCU1101 4 4
VCU1102 4 4
VCU1105 4 4
VCU1106 4 4
VCU1107 4 4
VCU1108 4 4
VCU1109 4 4
VCU1110 4 4
VCU1112 4 4
VCU1113 4 4
VCU1114 4 4
VCU1115 4 4
VCU1117 4 4
VCU1118 4 4
VCU1120 4 4
VCU1121 4 4
VCU1122 4 4
VCU1123 4 4
VCU1124 4 4
VCU1126 4 4
VCU1128 4 4
VCU1129 4 4
VCU1130 4 4
VCU1131 4 4
VCU1134 4 4
~~~~~~~~~~~~~~
lop$nSubj vs stimulus:
fear neu place pos
VCU1001 2 2 2 2
VCU1002 2 2 2 2
VCU1003 2 2 2 2
VCU1004 2 2 2 2
VCU1005 2 2 2 2
VCU1007 2 2 2 2
VCU1008 2 2 2 2
VCU1009 2 2 2 2
VCU1010 2 2 2 2
VCU1011 2 2 2 2
VCU1012 2 2 2 2
VCU1013 2 2 2 2
VCU1014 2 2 2 2
VCU1017 2 2 2 2
VCU1019 2 2 2 2
VCU1020 2 2 2 2
VCU1021 2 2 2 2
VCU1022 2 2 2 2
VCU1024 2 2 2 2
VCU1025 2 2 2 2
VCU1026 2 2 2 2
VCU1027 2 2 2 2
VCU1028 2 2 2 2
VCU1029 2 2 2 2
VCU1030 2 2 2 2
VCU1031 2 2 2 2
VCU1032 2 2 2 2
VCU1033 2 2 2 2
VCU1036 2 2 2 2
VCU1037 2 2 2 2
VCU1038 2 2 2 2
VCU1039 2 2 2 2
VCU1040 2 2 2 2
VCU1041 2 2 2 2
VCU1042 2 2 2 2
VCU1043 2 2 2 2
VCU1044 2 2 2 2
VCU1045 2 2 2 2
VCU1046 2 2 2 2
VCU1047 2 2 2 2
VCU1048 2 2 2 2
VCU1049 2 2 2 2
VCU1050 2 2 2 2
VCU1051 2 2 2 2
VCU1054 2 2 2 2
VCU1055 2 2 2 2
VCU1056 2 2 2 2
VCU1057 2 2 2 2
VCU1058 2 2 2 2
VCU1059 2 2 2 2
VCU1060 2 2 2 2
VCU1061 2 2 2 2
VCU1062 2 2 2 2
VCU1063 2 2 2 2
VCU1065 2 2 2 2
VCU1066 2 2 2 2
VCU1067 2 2 2 2
VCU1068 2 2 2 2
VCU1069 2 2 2 2
VCU1070 2 2 2 2
VCU1071 2 2 2 2
VCU1072 2 2 2 2
VCU1073 2 2 2 2
VCU1074 2 2 2 2
VCU1075 2 2 2 2
VCU1076 2 2 2 2
VCU1077 2 2 2 2
VCU1078 2 2 2 2
VCU1079 2 2 2 2
VCU1080 2 2 2 2
VCU1082 2 2 2 2
VCU1083 2 2 2 2
VCU1084 2 2 2 2
VCU1085 2 2 2 2
VCU1086 2 2 2 2
VCU1087 2 2 2 2
VCU1088 2 2 2 2
VCU1089 2 2 2 2
VCU1090 2 2 2 2
VCU1091 2 2 2 2
VCU1094 2 2 2 2
VCU1095 2 2 2 2
VCU1096 2 2 2 2
VCU1098 2 2 2 2
VCU1099 2 2 2 2
VCU1101 2 2 2 2
VCU1102 2 2 2 2
VCU1105 2 2 2 2
VCU1106 2 2 2 2
VCU1107 2 2 2 2
VCU1108 2 2 2 2
VCU1109 2 2 2 2
VCU1110 2 2 2 2
VCU1112 2 2 2 2
VCU1113 2 2 2 2
VCU1114 2 2 2 2
VCU1115 2 2 2 2
VCU1117 2 2 2 2
VCU1118 2 2 2 2
VCU1120 2 2 2 2
VCU1121 2 2 2 2
VCU1122 2 2 2 2
VCU1123 2 2 2 2
VCU1124 2 2 2 2
VCU1126 2 2 2 2
VCU1128 2 2 2 2
VCU1129 2 2 2 2
VCU1130 2 2 2 2
VCU1131 2 2 2 2
VCU1134 2 2 2 2
***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++
Error in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) :
invalid non-character version specification 'x' (type: double)
Calls: Ops.numeric_version ... as.numeric_version -> numeric_version -> .make_numeric_version
Execution halted
[eazuniga1@carimri-ws3 scripts]$
Script code:
#! /bin/csh
# to generate group maps of Emotional Faces task data using 3dMVM to accommodate different cell sizes
if ( -e group-diffs_NBack+tlrc.BRIK ) then
rm -rf group-diffs_NBack+*
endif
3dMVM -prefix group-diffs_NBack -jobs 16 \
-bsVars 'group' \
-wsVars 'mem_demand*stimulus' \
-mask groupmap-mask+tlrc \
-num_glt 24 \
-gltLabel 1 2bk_vs_0bk -gltCode 1 'mem_demand : 1*2-back -1*0-back' \
-gltLabel 2 facesVplaces -gltCode 2 'stimulus : .33*pos .33*neu .33*fear -1*place' \
-gltLabel 3 fearVneu -gltCode 3 'stimulus : 1*fear -1*neu ' \
-gltLabel 4 happyVneu -gltCode 4 'stimulus : 1*pos -1*neu ' \
-gltLabel 5 memdemand_heroinVcont -gltCode 5 'group : 1*heroin -1*control mem_demand : 1*2-back -1*0-back' \
-gltLabel 6 memdemand_amphVcont -gltCode 6 'group : 1*amph -1*control mem_demand : 1*2-back -1*0-back' \
-gltLabel 7 memdemand_polyVcont -gltCode 7 'group : 1*poly -1*control mem_demand : 1*2-back -1*0-back' \
-gltLabel 8 memdemand_AllSUDVcont -gltCode 8 'group : .33*heroin .33*amph .33*poly -1*control mem_demand : 1*2-back -1*0-back' \
-gltLabel 9 memdemand_amphVheroin -gltCode 9 'group : 1*amph -1*heroin mem_demand : 1*2-back -1*0-back' \
-gltLabel 10 facesVplaces_heroinVcont -gltCode 10 'group : 1*heroin -1*control stimulus : .33*pos .33*neu .33*fear -1*place' \
-gltLabel 11 facesVplaces_amphVcont -gltCode 11 'group : 1*amph -1*control stimulus : .33*pos .33*neu .33*fear -1*place' \
-gltLabel 12 facesVplaces_polyVcont -gltCode 12 'group : 1*poly -1*control stimulus : .33*pos .33*neu .33*fear -1*place' \
-gltLabel 13 facesVplaces_allSUDVcont -gltCode 13 'group : 33*heroin .33*amph .33*poly -1*control stimulus : .33*pos .33*neu .33*fear -1*place' \
-gltLabel 14 facesVplaces_amphVheroin -gltCode 14 'group : 1*amph -1*heroin stimulus : .33*pos .33*neu .33*fear -1*place' \
-gltLabel 15 fearVneu_heroinVcont -gltCode 15 'group : 1*heroin -1*control stimulus : 1*fear -1*neu' \
-gltLabel 16 fearVneu_amphVcont -gltCode 16 'group : 1*amph -1*control stimulus : 1*fear -1*neu' \
-gltLabel 17 fearVneu_heroinVcont -gltCode 17 'group : 1*poly -1*control stimulus : 1*fear -1*neu' \
-gltLabel 18 fearVneu_AllSUDVcont -gltCode 18 'group : .33*heroin .33*amph .33*poly -1*control stimulus : 1*fear -1*neu' \
-gltLabel 19 fearVneu_amphVheroin -gltCode 19 'group : 1*amph -1*heroin stimulus : 1*fear -1*neu' \
-gltLabel 20 happyVneu_heroinVcont -gltCode 20 'group : 1*heroin -1*control stimulus : 1*pos -1*neu' \
-gltLabel 21 happyVneu_amphVcont -gltCode 21 'group : 1*amph -1*control stimulus : 1*pos -1*neu' \
-gltLabel 22 happyVneu_heroinVcont -gltCode 22 'group : 1*poly -1*control stimulus : 1*pos -1*neu' \
-gltLabel 23 happyVneu_AllSUDVcont -gltCode 23 'group : .33*heroin .33*amph .33*poly -1*control stimulus : 1*pos -1*neu' \
-gltLabel 24 happyVneu_amphVheroin -gltCode 24 'group : 1*amph -1*heroin stimulus : 1*pos -1*neu' \
-dataTable @3dMVM-DataTable-NBack.txt
mv group-diffs_NBack* ../NBgroupmaps
AFNI System Check:
[eazuniga1@carimri-ws3 scripts]$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type: x86_64
system: Linux
release: 4.18.0-553.5.1.el8_10.x86_64
version: #1 SMP Thu Jun 6 09:41:19 UTC 2024
distribution: Rocky Linux 8.10 (Green Obsidian)
number of CPUs: 16
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /usr/local/software/afni/abin/afni
afni version : Precompiled binary linux_rocky_8: Apr 2 2024
: AFNI_24.1.00 'Publius Septimius Geta'
AFNI_version.txt : AFNI_24.1.00, linux_rocky_8, Apr 02 2024, official
which python : /usr/local/software/miniconda3/envs/py3_afni_tiny/bin/python
python version : 3.12.3
which R : /usr/bin/R
R version : R version 4.4.0 (x86_64-redhat-linux-gnu)
instances of various programs found in PATH:
afni : 1 (/usr/local/software/afni/abin/afni)
R : 1 (/usr/bin/R)
python : 2
/usr/local/software/miniconda3/envs/py3_afni_tiny/bin/python3.12
/usr/bin/python3.11
python2 : 0
python3 : 2
/usr/local/software/miniconda3/envs/py3_afni_tiny/bin/python3.12
/usr/libexec/platform-python3.6
** have python3 but not python2
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
uber_subject.py : success
3dMVM : success
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /usr/bin/tcsh
which Xvfb : /usr/bin/Xvfb
checking for R packages...
rPkgsInstall -pkgs ALL -check : success
R RHOME : /usr/lib64/R
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /usr/local/software/miniconda3/envs/py3_afni_tiny/lib/python3.12/site-packages/matplotlib/pyplot.py
matplotlib version : 3.8.4
++ module loaded: flask
module file : /usr/local/software/miniconda3/envs/py3_afni_tiny/lib/python3.12/site-packages/flask/__init__.py
flask version : 3.0.3
++ module loaded: flask_cors
module file : /usr/local/software/miniconda3/envs/py3_afni_tiny/lib/python3.12/site-packages/flask_cors/__init__.py
flask_cors version : 3.0.10
-------------------------------- env vars --------------------------------
PATH = /usr/local/cuda-12.2/bin:/usr/local/software/fsl/share/fsl/bin:/usr/local/software/fsl/share/fsl/bin:/usr/local/cuda-12.2/bin:/usr/local/software/fsl/share/fsl/bin:/usr/local/software/fsl/share/fsl/bin:/home/eazuniga1/.local/bin:/home/eazuniga1/bin:/usr/local/software/miniconda3/envs/py3_afni_tiny/bin:/usr/local/software/miniconda3/condabin:/usr/local/cuda-12.2/bin:/usr/local/software/fsl/share/fsl/bin:/usr/local/software/fsl/share/fsl/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/software/afni/abin:/usr/local/bin/matlab:/opt/puppetlabs/bin:/usr/local/software/afni/abin:/usr/local/bin/matlab:/usr/local/software/afni/abin:/usr/local/bin/matlab
PYTHONPATH =
R_LIBS = /usr/local/software/afni/R
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
CONDA_SHLVL = 2
CONDA_DEFAULT_ENV = py3_afni_tiny
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
--------- shell startup files ----------
-- no .tcshrc, will create one as a follower of .cshrc
-- considered operations: path, apsearch
-- note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)
dot file test : want 4 modifications across 3 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.cshrc 1 0 1 0
.tcshrc 0 0 0 1
.bashrc 1 0 1 0
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /usr/local/software/afni/abin
------------------------------ OS specific -------------------------------
which dnf : /usr/bin/dnf
dnf version : 4.7.0
which yum : /usr/bin/yum
yum version : 4.7.0
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* dot file test : want 4 modifications across 3 files:
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)
[eazuniga1@carimri-ws3 scripts]$