3dLME Error

AFNI Message Board
1

Hello,

I receive the following error when trying to run a 3dLME script:
Error in (pos[ii] + 1):(pos[ii + 1] - 2) : NA/NaN argument
Calls: process.LME.opts → gl_Constr → glfConstr → which
Execution halted

I used rPkgsInstall -pkgs ALL to install the R packages. I am using a linux system, AFNI Version AFNI_21.0.21 ‘Titus’, and R version 4.0.5 (2021-03-31). Do you know what might be causing this error?

2

Could you share your 3dLME script? It’s fine to only include a few lines of the data table.

3

Was there ever a solution to this? I’m having the same issue, and have checked all my R packages and run afni_system_check.py and have found nothing amiss.

4

My request remains the same: Could you share your 3dLME script with a few lines of the data table?

5

I've also encountered this error. AFNI & R have been updated.

afni_vcheck
This program was compiled with the following settings:
Version ID = AFNI_24.0.02
++ now fetching https://afni.nimh.nih.gov/pub/dist/AFNI.version
Latest version listed at AFNI web site:
Version ID = AFNI_24.0.06

R version:
platform aarch64-apple-darwin20
arch aarch64
os darwin20
system aarch64, darwin20
status
major 4
minor 3.1
year 2023
month 06
day 16
svn rev 84548
language R
version.string R version 4.3.1 (2023-06-16)
nickname Beagle Scouts

My script:

3dLME -prefix 3dLME_output_Format_Quantity \

-jobs 12 -mask /Users/andrewlynn/Documents/Projects/HomeMath_RSA/ref/mask/BN_Atlas_HaskinsPeds_NL_template_2.5_mask+tlrc.HEAD \

-model "format*quantity" \

-ranEff "~1" \

-SS_type 3 \

-num_glt 2 \

-gltLabel 1 LinearQuant -gltcode 1 "quantity : 3*seven 2*six 1*five -1*four -2*three -3*two" \

-gltLabel 2 FormatLinearQuant -gltcode 2 "format : 1*digit -1*dot quantity : 3*seven 2*six 1*five -1*four -2*three -3*two" \

-dataTable \

Subj format quantity InputFile \

DDK2001 digit two /Users/andrewlynn/Documents/Projects/HomeMath_RSA/Processed_Data/DDK2001/Y1/proc/exemplar.stats.DDK2001+tlrc"[Digit_2#0_Coef]" \

DDK2001 digit three /Users/andrewlynn/Documents/Projects/HomeMath_RSA/Processed_Data/DDK2001/Y1/proc/exemplar.stats.DDK2001+tlrc"[Digit_3#0_Coef]" \

DDK2001 digit four /Users/andrewlynn/Documents/Projects/HomeMath_RSA/Processed_Data/DDK2001/Y1/proc/exemplar.stats.DDK2001+tlrc"[Digit_4#0_Coef]" \

DDK2001 digit five /Users/andrewlynn/Documents/Projects/HomeMath_RSA/Processed_Data/DDK2001/Y1/proc/exemplar.stats.DDK2001+tlrc"[Digit_5#0_Coef]" \

DDK2001 digit six /Users/andrewlynn/Documents/Projects/HomeMath_RSA/Processed_Data/DDK2001/Y1/proc/exemplar.stats.DDK2001+tlrc"[Digit_6#0_Coef]" \

DDK2001 digit seven /Users/andrewlynn/Documents/Projects/HomeMath_RSA/Processed_Data/DDK2001/Y1/proc/exemplar.stats.DDK2001+tlrc"[Digit_7#0_Coef]" \

DDK2001 dot two /Users/andrewlynn/Documents/Projects/HomeMath_RSA/Processed_Data/DDK2001/Y1/proc/exemplar.stats.DDK2001+tlrc"[Dots_2#0_Coef]" \

DDK2001 dot three /Users/andrewlynn/Documents/Projects/HomeMath_RSA/Processed_Data/DDK2001/Y1/proc/exemplar.stats.DDK2001+tlrc"[Dots_3#0_Coef]" \

DDK2001 dot four /Users/andrewlynn/Documents/Projects/HomeMath_RSA/Processed_Data/DDK2001/Y1/proc/exemplar.stats.DDK2001+tlrc"[Dots_4#0_Coef]" \

DDK2001 dot five /Users/andrewlynn/Documents/Projects/HomeMath_RSA/Processed_Data/DDK2001/Y1/proc/exemplar.stats.DDK2001+tlrc"[Dots_5#0_Coef]" \

DDK2001 dot six /Users/andrewlynn/Documents/Projects/HomeMath_RSA/Processed_Data/DDK2001/Y1/proc/exemplar.stats.DDK2001+tlrc"[Dots_6#0_Coef]" \

DDK2001 dot seven /Users/andrewlynn/Documents/Projects/HomeMath_RSA/Processed_Data/DDK2001/Y1/proc/exemplar.stats.DDK2001+tlrc"[Dots_7#0_Coef]" \```
6

This appears to be related to a minor typo. That is, the capitalized "C" in "-gltCode" is important! In my code I had typed "-gltcode"

Changing the c to a C seems to solve the problem.

7

@andrewlynnphd
In addition to the typo, there are issues with the model specification. If both factors, format and quantity, are within-individual, I recommend employing 3dLMEr and following the guidelines outlined in this instruction. Alternatively, you can use 3dMVM if no missing data occur.

Gang Chen