AFNI 3dISC Hung Up Command Line After Loading Packages

AFNI Message Board
1

Hello! When trying to run AFNI's 3dISC function using Linux, we have run into an issue where the command line begins hanging after loading in the required packages (lme4 and Matrix). We are using a model that we have used numerous times before with the 3dISC command, so we know that our model for the 3dISC command is not the issue, but I will provide all the model information below regardless.

Once we run our 3dISC, it successfully summarizes the information of the data structure (***** Summary information of data structure *****), and centers values for numeric variable grp (903 centered values for numeric variable grp). Next, this is what it says:

Contingency tables of subject distributions among the categorical variables:

***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++

Reading input files now...

Reading input files for effect estimates: Done!

Range of input data: [-0.610, 0.864]

If the program hangs here for more than, for example, half an hour, kill the process because the model specification or something else is likely inappropriate.

Loading required package: lme4
Loading required package: Matrix

This is where it stops running, but rather than terminating the process, it just hangs there and doesn't give us any error messages.

Below is the model that we specified after 3dISC and our prefix:
-jobs 5 -model 'FSA+(1|Subj1)+(1|Subj2)' -qVars 'FSA' -gltCode ave '1 0' -gltCode FSA '0 1' -dataTable Subj1 Subj2 FSA InputFile

Again, we have used this exact model several times successfully using 3dISC, so we are at a loss for what could be causing this issue. Any help would be greatly appreciated!

2

What is the output of running the following at the terminal?

R --version
R -e 'packageVersion("lme4")'
R -e 'packageVersion("Matrix")'

Gang Chen

3

Thank you for your quick response!

For R --version, the output is:

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

For R -e 'packageVersion("lme4")' the output is:

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

packageVersion("lme4")
[1] ‘1.1.32’

For R -e 'packageVersion("Matrix")'

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

packageVersion("Matrix")
[1] ‘1.6.5’

4

Thanks for sharing the information. Try updating the following packages in R:

install.packages("lme4")
install.packages("Matrix")

Then execute your 3dISC script.

If the problem persists, would it be possible to provide some demo data along with the 3dISC script? If so, please feel free to contact me via email.

Gang Chen

5

After updated the packages it started working! Thank you so much for your help!