3dmvm -data table not rectangular

AFNI Message Board
1

Hello,

Thank you in advance for any help you can provide. I am running into several issues with 3dMVM. Below is my code.

3dMVM -prefix WholeBrain_MVM_Contrasts5 -jobs 12
-bsVars Weight
-wsVars Reward \
-num_glt 3 \
-gltlabel 1 -gltCode 1 ’Weight : 1HW -1OW Reward : 1FA -1NA’ \
-gltlabel 2 -gltCode 2 ‘Weight : 1HW -1OW Reward : 1FA -1MA’ \
-gltlabel 3 -gltCode 3 ‘Weight : 1HW -1OW Reward : 1MA -1NA’ \
-dataTable
Subj Weight Age Sex Reward InputFile
101 OW 10 F FA stats.101+tlrc’[1]’ \
101 OW 10 F MA stats.101+tlrc’[4]’
101 OW 10 F NA stats.101+tlrc’[7]’
102 OW 8 M FA stats.102+tlrc’[1]’
102 OW 8 M MA stats.102+tlrc’[4]’
102 OW 8 M NA stats.102+tlrc’[7]’
103 HW 7 F FA stats.103+tlrc’[1]’
103 HW 7 F MA stats.103+tlrc’[4]’
103 HW 7 F NA stats.103+tlrc’[7]’ \

  1. When I run the code as such, I get the error a) data table is not rectangular b) num_glt command not found, c) gltlabel: no match d)-dataTable command not found.

  2. If I remove num_glt + the gltlabels, the script will run. However, I just get one .BRIK and .HEAD file named WholeBrain_MVM_Contrasts5. I am unaware of how to see the effects of my interactions etc.

  3. The stats.$subj+tlrc’[#]’ corresponds to my stats file from my preprocessing stream (using uber_subject) and sub-brick number[#] of the condition that I want to extract

I’ve tried lots of variations and have also extracted the specific sub-bricks that I wanted and tried to use those as InputFiles (e.g. $subj#_FA_betas+tlrc’[FA#0_Coef]’ but this also seems to give the above errors.

Thanks for your help,
Shana

2

Shana,

The 3 occurrences of “gltlabel” should be “gltLabel”. Also you need to provide a real label for each GLT with something like

-gltLabel 1 myGLT1 …

If you still get an error of “num_glt command not found”, run the following command at the terminal and see if it gives you some hint:

file_tool -test -infile your3dMVMscript

3

Hi Gang,

Thank you for your quick reply. I fixed my code:

3dMVM -prefix WholeBrain_MVM_Contrasts5 -jobs 12 \
—bsVars Weight \
-wsVars Reward \
-num_glt 3 \
-gltLabel 1 ‘weight_F_N’ -gltCode 1 ’Weight : 1HW -1OW Reward : 1FA -1NA’
-gltLabel 2 ‘weight_F_M’ -gltCode 2 ‘Weight : 1HW -1OW Reward : 1FA -1MA’
-gltLabel 3 ‘weight_M_N’ -gltCode 3 ‘Weight : 1HW -1OW Reward : 1MA -1NA’
-dataTable
101 OW 10 F FA stats.101+tlrc’[1]’ \
101 OW 10 F MA stats.101+tlrc’[4]’ \
101 OW 10 F NA stats.101+tlrc’[7]’ \
102 OW 8 M FA stats.102+tlrc’[1]’ \
102 OW 8 M MA stats.102+tlrc’[4]’ \
102 OW 8 M NA stats.102+tlrc’[7]’ \
103 HW 7 F FA stats.103+tlrc’[1]’ \
103 HW 7 F MA stats.103+tlrc’[4]’ \
103 HW 7 F NA stats.103+tlrc’[7]’ \
…

Your suggestion to use file_tool -test -infile myfile was helpful. However, the only thing that I found is that I have bad '' and no matter how I try to fix my '' it still gives me errors. If I use: file_tool -show_bad_backslash -infile myfile.txt -prefix FIXED.txt, this creates a problem as when I try to run the “FIXED.txt”, it says 3dMVM : No match. Pasting this script with the corrected or fixed '' (they look exactly the same, into another document creates the same problem.