Specifying 3dLMEr; not reading in correctly? stuck in loading packages


I’m having trouble with 3dLMEr. I am working with a dataset in which each participant watched a movie, and for each movie I have a regressor representing the extracted “sentiment.” I have .nii.gz outputs from 3dDeconvolve for each subject, and now I’d like to look at the effect of that sentiment arc across all movies where I specify subjects and movies as random factors.

Here is the script I’m working with so far with a subset of participants…


3dLMEr -prefix LME
-model ‘(1|Subj)+(1|movie)’
Subj movie InputFile
sub02 500daysofsummer stats_500daysofsummer.sub-02.nii.gz’[audio_arc#0_Coef]’
sub04 500daysofsummer stats_500daysofsummer.sub-04.nii.gz’[audio_arc#0_Coef]’
sub39 usualsuspects stats_usualsuspects.sub-39.nii.gz’[audio_arc#0_Coef]’
sub41 usualsuspects stats_usualsuspects.sub-41.nii.gz’[audio_arc#0_Coef]’
sub48 pulpfiction stats_pulpfiction.sub-48.nii.gz’[audio_arc#0_Coef]’
sub50 pulpfiction stats_pulpfiction.sub-50.nii.gz’[audio_arc#0_Coef]’
sub51 shawshankredemption stats_shawshankredemption.sub-51.nii.gz’[audio_arc#0_Coef]’
sub52 shawshankredemption stats_shawshankredemption.sub-52.nii.gz’[audio_arc#0_Coef]’
sub60 theprestige stats_theprestige.sub-60.nii.gz’[audio_arc#0_Coef]’
sub62 theprestige stats_theprestige.sub-62.nii.gz’[audio_arc#0_Coef]’
sub63 backtothefuture stats_backtothefuture.sub-63.nii.gz’[audio_arc#0_Coef]’
sub68 backtothefuture stats_backtothefuture.sub-68.nii.gz’[audio_arc#0_Coef]’
sub81 12yearsaslave stats_12yearsaslave.sub-81.nii.gz’[audio_arc#0_Coef]’
sub86 12yearsaslave stats_12yearsaslave.sub-86.nii.gz’[audio_arc#0_Coef]’

When running this script, I get the following output that shows a few noticeable things… There is nothing listed on “contingency tables…among the categorical variables” and the range of input data shows -0.0, 0.001. It then gets stuck trying to load R packages.

***** Summary information of data structure *****
38 response values

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: [-0.000, 0.001]

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: lmerTest
Loading required package: lme4
Loading required package: Matrix

Attaching package: ‘lmerTest’

The following object is masked from ‘package:lme4’:


The following object is masked from ‘package:stats’:


Loading required package: phia
Loading required package: car
Loading required package: carData
Registered S3 methods overwritten by ‘car’:
method from
influence.merMod lme4
cooks.distance.influence.merMod lme4
dfbeta.influence.merMod lme4
dfbetas.influence.merMod lme4

I’ve looked at my individual subject images, and everything looks normal. I’ve looked into my R installation and everything seems to be installed appropriately (R version 3.6.3 as recommended on the afni installation page). I’ve tested out a few different versions of quotes around the InputFiles to no avail. Ultimately, I’m not sure if I’m specifying something wrong in the script, there is an R problem, or it’s something else entirely! (I’m new to afni). Can you help?

Thank you!

You have an unusual situation where there are no “fixed” effects other than the intercept. I may have to modify 3dLMEr to adapt to such a special scenario.