3dMVM

AFNI Message Board
1

Good afternoon,

I am having trouble running my 3dMVM script, likely due to a typo but I don’t seem able to identify it. The error I get back says:

Error in [.data.frame(lop$dataStr, , jj) : undefined columns selected
Calls: process.MVM.opts → [ → [.data.frame

Attached is the script:

dMVM -prefix MVM_Group_Results -jobs 1
-bsVars ‘group+Symptoms’
-qVars ‘Symptoms’
-mask mask_resamp+tlrc.
-SS_type 3
-num_glt 6
-gltLabel 1 Baseline_ETOH+vsETOH- -gltCode 1 ‘group : 1Baseline_ETOH+ -1Baseline_ETOH-’
-gltLabel 2 Post_ETOH+vsETOH- -gltCode 2 ‘group : 1Post_ETOH+ -1Post_ETOH-’
-gltLabel 3 Baseline_ETOH+vsHV -gltCode 3 ‘group : 1Baseline_ETOH+ -1HV’
-gltLabel 4 Baseline_ETOH-vsHV -gltCode 4 ‘group : 1Baseline_ETOH- -1HV’
-gltLabel 5 Post_ETOH+vsHV -gltCode 5 ‘group : 1Post_ETOH+ -1HV’
-gltLabel 6 Post_ETOH-vsHV -gltCode 6 ‘group : 1Post_ETOH+ -1HV’
-dataTable @Cfile-MVM.txt

Attached is dataTable:

Subj Group Severity InputFile
s102 Baseline_ETOH+ 1.03 /Volumes/19-1680/Lena_ETOH/Stat_files/1_Baseline/stats.s102+tlrc’[7]’
s104 Baseline_ETOH+ 2.43 /Volumes/19-1680/Lena_ETOH/Stat_files/1_Baseline/stats.s104+tlrc’[7]’
s105 Baseline_ETOH+ 1.13 /Volumes/19-1680/Lena_ETOH/Stat_files/1_Baseline/stats.s105+tlrc’[7]’
…
s103 HV 0.00 /Volumes/19-1680/Lena_ETOH/Stat_files/HV/stats.s103+tlrc’[4]’
s104 HV 0.00 /Volumes/19-1680/Lena_ETOH/Stat_files/HV/stats.s104+tlrc’[4]’
s105 HV 0.00 /Volumes/19-1680/Lena_ETOH/Stat_files/HV/stats.s105+tlrc’[4]’
s106 HV 0.00 /Volumes/19-1680/Lena_ETOH/Stat_files/HV/stats.s106+tlrc’[4]’
s114 HV 0.00 /Volumes/19-1680/Lena_ETOH/Stat_files/HV/stats.s114+tlrc’[4]’
s115 HV 0.00 /Volumes/19-1680/Lena_ETOH/Stat_files/HV/stats.s115+tlrc’[4]’
s116 HV 0.00 /Volumes/19-1680/Lena_ETOH/Stat_files/HV/stats.s116+tlrc’[4]’
s117 HV 0.00 /Volumes/19-1680/Lena_ETOH/Stat_files/HV/stats.s117+tlrc’[4]’
s119 HV 0.00 /Volumes/19-1680/Lena_ETOH/Stat_files/HV/stats.s119+tlrc’[4]’
s120 HV 0.00 /Volumes/19-1680/Lena_ETOH/Stat_files/HV/stats.s120+tlrc’[4]’

Thanks,
Lena

2

Hi, Lena-

I think the issue might be that if you are using a dataTable file, the contents of that file should not have a quote around the subbrick selectors, nor does there need to be the continuation-of-line characters "" at the end of each line.

Note that the syntax of your current table—with those apostrophes and ""s—would be correct if being used directly as part of the 3dMVM command in the shell. Those special characters are needed because of going through the shell interpreter to get to AFNI.

So, I would make a copy of that data table, and remove the single quotes and the backslashes, and see if that solves it.

–pt

3

Instead, I moved the table contents to the same script. Unfortunately, I I am still getting the error:

updating R_LD_LIBRARY_PATH …
Error in [.data.frame(lop$dataStr, , jj) : undefined columns selected
Calls: process.MVM.opts → [ → [.data.frame
Execution halted

Attached is the script:

3dMVM -prefix MVM_Group_Results -jobs 1
-bsVars ‘group+Symptoms’
-qVars ‘Symptoms’
-mask mask_resamp+tlrc.
-SS_type 3
-num_glt 6
-gltLabel 1 Baseline_ETOH+vsETOH- -gltCode 1 ‘group : 1Baseline_ETOH+ -1Baseline_ETOH-’
-gltLabel 2 Post_ETOH+vsETOH- -gltCode 2 ‘group : 1Post_ETOH+ -1Post_ETOH-’
-gltLabel 3 Baseline_ETOH+vsHV -gltCode 3 ‘group : 1Baseline_ETOH+ -1HV’
-gltLabel 4 Baseline_ETOH-vsHV -gltCode 4 ‘group : 1Baseline_ETOH- -1HV’
-gltLabel 5 Post_ETOH+vsHV -gltCode 5 ‘group : 1Post_ETOH+ -1HV’
-gltLabel 6 Post_ETOH-vsHV -gltCode 6 ‘group : 1Post_ETOH+ -1HV’
-dataTable
Subj Group Severity InputFile
s102 Baseline_ETOH+ 1.03 /Volumes/19-1680/Lena_ETOH/Stat_files/1_Baseline/stats.s102+tlrc’[7]’
s104 Baseline_ETOH+ 2.43 /Volumes/19-1680/Lena_ETOH/Stat_files/1_Baseline/stats.s104+tlrc’[7]’
s105 Baseline_ETOH+ 1.13 /Volumes/19-1680/Lena_ETOH/Stat_files/1_Baseline/stats.s105+tlrc’[7]’
s106 Baseline_ETOH+ 3.65 /Volumes/19-1680/Lena_ETOH/Stat_files/1_Baseline/stats.s106+tlrc’[7]’
s107 Baseline_ETOH+ 3.28 /Volumes/19-1680/Lena_ETOH/Stat_files/1_Baseline/stats.s107+tlrc’[7]’
…
s104 HV 0.00 /Volumes/19-1680/Lena_ETOH/Stat_files/HV/stats.s104+tlrc’[4]’
s105 HV 0.00 /Volumes/19-1680/Lena_ETOH/Stat_files/HV/stats.s105+tlrc’[4]’
s106 HV 0.00 /Volumes/19-1680/Lena_ETOH/Stat_files/HV/stats.s106+tlrc’[4]’
s114 HV 0.00 /Volumes/19-1680/Lena_ETOH/Stat_files/HV/stats.s114+tlrc’[4]’
s115 HV 0.00 /Volumes/19-1680/Lena_ETOH/Stat_files/HV/stats.s115+tlrc’[4]’
s116 HV 0.00 /Volumes/19-1680/Lena_ETOH/Stat_files/HV/stats.s116+tlrc’[4]’
s117 HV 0.00 /Volumes/19-1680/Lena_ETOH/Stat_files/HV/stats.s117+tlrc’[4]’
s119 HV 0.00 /Volumes/19-1680/Lena_ETOH/Stat_files/HV/stats.s119+tlrc’[4]’
s120 HV 0.00 /Volumes/19-1680/Lena_ETOH/Stat_files/HV/stats.s120+tlrc’[4]’

Thank you for your help,
Lena

4

The top part describes group and Symptoms but the dataTable specifies Severity.
Maybe that is causing the problem.

  • rick
5

In addition to what Rick pointed out, change the column name “Group” in the table to “group”.

6

Had to troubleshoot a couple more things, but the code really did not like group with a capital G! The script is running beautifully now.

Thank you for your help,
Lena