3dISC endlessly running when inputting many variables

AFNI Message Board
1

When attempting to run this script on a SLURM cluster on a single node, it endlessly runs without producing any output or error message. Near-identical code, just with less variables, ran without any problems. I am using a neurodocker container for afni and am using a conda environment to provide the R packages snow (version 0.4_4) and lme4 (version 1.1_34).

AFNI version info (afni -ver):

Precompiled binary linux_openmp_64: Oct 19 2020 (Version AFNI_20.3.01 'Vespasian')

Code

#!/bin/bash
singularity exec -B /home/scripts /home/scripts/afni-latest.sif /opt/afni-latest/3dISC \
    -prefix ALL \
    -jobs 20 \
    -model 'FlankerUncorrectedStandardScore+CardSortUncorrectedStandardScore+PositiveAffect+GeneralLifeSatisfaction+MeaningandPurpose+SelfEfficacy+PerceivedStress+FearAffect+FearSomaticArousal+Sadness+AngerAffect+AngerPhysicalAggression+EmotionalSupport+InstrumentalSupport+Friendship+Loneliness+PerceivedRejection+PerceivedHostility+AngerHostility+Age+EducationCode+MotherEducationCode+(1|Subj1)+(1|Subj2)' \
    -qVars 'FlankerUncorrectedStandardScore,CardSortUncorrectedStandardScore,PositiveAffect,GeneralLifeSatisfaction,MeaningandPurpose,SelfEfficacy,PerceivedStress,FearAffect,FearSomaticArousal,Sadness,AngerAffect,AngerPhysicalAggression,EmotionalSupport,InstrumentalSupport,Friendship,Loneliness,PerceivedRejection,PerceivedHostility,AngerHostility,Age,EducationCode,MotherEducationCode' \
    -gltCode ave '1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0' \
    -gltCode FlankerUncorrectedStandardScore '0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0' \
    -gltCode CardSortUncorrectedStandardScore '0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0' \
    -gltCode PositiveAffect '0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0' \
    -gltCode GeneralLifeSatisfaction '0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0' \
    -gltCode MeaningandPurpose '0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0' \
    -gltCode SelfEfficacy '0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0' \
    -gltCode PerceivedStress '0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0' \
    -gltCode FearAffect '0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0' \
    -gltCode FearSomaticArousal '0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0' \
    -gltCode Sadness '0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0' \
    -gltCode AngerAffect '0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0' \
    -gltCode AngerPhysicalAggression '0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0' \
    -gltCode EmotionalSupport '0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0' \
    -gltCode InstrumentalSupport '0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0' \
    -gltCode Friendship '0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0' \
    -gltCode Loneliness '0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0' \
    -gltCode PerceivedRejection '0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0' \
    -gltCode PerceivedHostility '0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0' \
    -gltCode AngerHostility '0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0' \
    -gltCode Age '0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0' \
    -gltCode EducationCode '0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0' \
    -gltCode MotherEducationCode '0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1' \
    -dataTable \
    Subj1 Subj2 FlankerUncorrectedStandardScore CardSortUncorrectedStandardScore PositiveAffect GeneralLifeSatisfaction MeaningandPurpose SelfEfficacy PerceivedStress FearAffect FearSomaticArousal Sadness AngerAffect AngerPhysicalAggression EmotionalSupport InstrumentalSupport Friendship Loneliness PerceivedRejection PerceivedHostility AngerHostility Age EducationCode MotherEducationCode InputFile \
    s11 s10 8.285714285714278 -9 22.17857142857143 18.89285714285714 25.89285714285714 9.75 -30.214285714285708 -27.35714285714286 -4.642857142857139 -23.25 -26.5 -9.75 20.35714285714286 7 20.92857142857143 -29.75 -11.642857142857139 -10.17857142857143 -13.357142857142861 -1.5714285714285694 -1.1095714285714284 -0.08621428571428624 sub-10_11+tlrc \
    s12 s10 5.285714285714278 9 -6.821428571428569 5.892857142857139 -13.107142857142861 -5.25 -3.214285714285708 -3.357142857142861 10.357142857142861 -11.25 8.5 -1.75 -16.64285714285714 -2 -15.07142857142857 8.25 28.35714285714286 21.82142857142857 3.642857142857139 -2.5714285714285694 -0.23057142857142843 2.8037857142857137 sub-10_12+tlrc \

(dataTable truncated)

2

Diagnosing the issue with 3dISC in your case is challenging without direct access to your data. Additionally, with 22 explanatory variables in your model, it may be beneficial to consider the causal relationships between these variables and the response variable. For information about proper covariate selection and potential pitfalls, refer to this blog post and the associated paper.

Gang Chen

3

We narrowed down the number of covariates but the same problem is still occurring. Is the model specification done properly? No error message is being provided.

#!/bin/bash
singularity exec -B /home/scratch/scripts /home/scratch/scripts/afni-latest.sif /opt/afni-latest/3dISC \
    -prefix SUM \
    -jobs 20 \
    -model 'at+emneg+empos+soneg+sopos+(1|Subj1)+(1|Subj2)' \
    -qVars 'at,emneg,empos,soneg,sopos' \
    -gltCode ave '1 0 0 0 0 0' \
    -gltCode at '0 1 0 0 0 0' \
    -gltCode emneg '0 0 1 0 0 0' \
    -gltCode empos '0 0 0 1 0 0' \
    -gltCode soneg '0 0 0 0 1 0' \
    -gltCode sopos '0 0 0 0 0 1' \
    -dataTable \
    Subj1 Subj2 at emneg empos soneg sopos InputFile \
    s11 s10 -0.357142857142861 -20.285714285714274 19.17857142857142 -16.23214285714283 16.09523809523815 sub-10_11+tlrc \
    s12 s10 7.142857142857139 -0.11904761904761349 -4.82142857142856 15.517857142857169 -11.238095238095251 sub-10_12+tlrc \
    s13 s10 0.1428571428571379 6.380952380952386 -0.07142857142856052 2.767857142857139 -3.5714285714285596 sub-10_13+tlrc \

(dataTable truncated)

4

Could you provide the version numbers for the following?

afni -ver
R --version
R -e 'packageVersion("lme4")'

Gang Chen

5 
afni -ver
Precompiled binary linux_ubuntu_24_64: Jul 16 2024 (Version AFNI_24.2.01 'Macrinus')

R --version
R version 4.4.3 (2025-02-28) -- "Trophy Case"

R -e 'packageVersion("lme4")'
[1] ‘1.1.35.5’