3dMVM eror question

AFNI Message Board
1

Dear AFNI experts,

I was trying to run the command below.

#!/bin/tcsh
3dMVM -prefix DBP_sitting_ATT_smoothing
-qVars 'age,sex,edu,bmi,menupause,med,dbp'
-bsVars 'age+sex+edu+bmi+menupause+med+dbp'
-num_glt 1
-gltLabel 1 'dbp' -gltCode 1 'dbp:'
-mask MNI152_T1_1mm_brain_64.nii.gz
-dataTable \
Subj age sex edu bmi menupause med dbp InputFile \

The script was running fine, but it shows the error below. Could you please advise what would be an issue?

Warning message:
package ‘data.table’ was built under R version 4.3.2

** Error:
Expecting 1 to 1e+06 parameters for option "-dataTable".
Have 0 parameter(s) in string "" instead.

** Error:
Error parsing arguments. See 3dMVM -help for details.
Subj: Command not found.

Best,
JW

2

JW,

Update your AFNI to the latest version. The recent updates include added functionality that may help detect abnormalities in the data table.

Gang Chen

3

Hi Gang,

Thank you. I actually have updated AFNI (@update.afni.binaries -defaults) before running the script and it is still showing the error. Could you please check if I have updated not a correct way?

-- running @update.afni.binaries version 3.24, December 7, 2023
-- have AFNI binaries under /Users/cvas/abin
-- have current build label official
-- install dir: using existing /Users/cvas/abin
-- any downloads will be from https://afni.nimh.nih.gov via curl -O -f

-- attempting to install package macos_10.12_local under
install dir: /Users/cvas/abin...
-- have install dir
++ working in new temp dir, .tmp.install
++ getting install prog: curl -O -f bin/misc/@update.afni.binaries ...
curl -O -f https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 53097 100 53097 0 0 109k 0 --:--:-- --:--:-- --:--:-- 111k
-- fixing lost permissions on @update.afni.binaries
-- @update.afni.binaries is current, continuing with this version...
++ downloading test file: curl -O -f macos_10.12_local/afni ...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 11.7M 100 11.7M 0 0 1762k 0 0:00:06 0:00:06 --:--:-- 2075k
++ no update needed

4

JW,

You may need to reinstall AFNI by following the instructions here.

Gang Chen

5

Hi Gang,

I reinstalled AFNI according to the instruction.
Precompiled binary macos_10.12_local: May 10 2024 (Version AFNI_24.1.11 'Publius Septimius Geta')

Also checked rPkgsInstall -pkgs ALL -check and all the packages are installed.

++ Note: @ 12:34:12
This package has been verified on the computer: afex
This package has been verified on the computer: phia
This package has been verified on the computer: snow
This package has been verified on the computer: nlme
This package has been verified on the computer: lme4
This package has been verified on the computer: lmerTest
This package has been verified on the computer: gamm4
This package has been verified on the computer: data.table
This package has been verified on the computer: paran
This package has been verified on the computer: psych
This package has been verified on the computer: brms
This package has been verified on the computer: corrplot
This package has been verified on the computer: metafor

But still have the error below. Please advise.

Warning message:
package ‘data.table’ was built under R version 4.3.2

** Error:
Expecting 1 to 1e+06 parameters for option "-dataTable".
Have 0 parameter(s) in string "" instead.

** Error:
Error parsing arguments. See 3dMVM -help for details.
Subj: Command not found.

Best,
JW

6

JW,

I suspect you have some empty space at the end of the following line in your 3dMVM script:

-dataTable \

Also, consider updating your R.

Gang Chen

7

Hi Gang,

As you mentioned, I found some empty space after -dataTable \ and after removing those, the script runs well. Thanks for your help.

Best,
JW