afni.nimh.nih.gov

Hello AFNI Experts,

I have a mixed design of Group (hc, sci) x Run (run1, run2) for which I wanted to use 3dLMEr (in case I don't have a balanced design in the end for 3dANOVA).

Below is the code that I have tested:

derivatives=/mnt/LABS/tbi/implicitmem_SCI/derivatives
outdir=$derivatives/3dLME
indir=/mnt/LABS/tbi/implicitmem_SCI/derivatives/feat_lev1_hp100
3dLMEr \
  -prefix ${outdir}/hp100 \
  -jobs 2 \
  -mask $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz \
  -model 'run*group+(1|Subj)' \
  -dataTable \
      Subj  run   group InputFile \
      sub-IPLHC201      run1  hc    $indir/sub-IPLHC201_run-1.feat/stats/cope4.nii.gz \
      sub-IPLHC201      run2  hc    $indir/sub-IPLHC201_run-2.feat/stats/cope4.nii.gz \
      sub-IPLHC202      run1  hc    $indir/sub-IPLHC202_run-1.feat/stats/cope4.nii.gz \
      sub-IPLHC202      run2  hc    $indir/sub-IPLHC202_run-2.feat/stats/cope4.nii.gz \
      sub-IPLHC203      run1  hc    $indir/sub-IPLHC203_run-1.feat/stats/cope4.nii.gz \
      sub-IPLHC203      run2  hc    $indir/sub-IPLHC203_run-2.feat/stats/cope4.nii.gz \
      sub-IPLHC206      run1  hc    $indir/sub-IPLHC206_run-1.feat/stats/cope4.nii.gz \
      sub-IPLHC206      run2  hc    $indir/sub-IPLHC206_run-2.feat/stats/cope4.nii.gz \
      sub-IPLSCI102     run1  sci   $indir/sub-IPLSCI102_run-1.feat/stats/cope4.nii.gz \
      sub-IPLSCI102     run2  sci   $indir/sub-IPLSCI102_run-2.feat/stats/cope4.nii.gz \
      sub-IPLSCI103     run1  sci   $indir/sub-IPLSCI103_run-1.feat/stats/cope4.nii.gz \
      sub-IPLSCI103     run2  sci   $indir/sub-IPLSCI103_run-2.feat/stats/cope4.nii.gz \
      sub-IPLSCI104     run1  sci   $indir/sub-IPLSCI104_run-1.feat/stats/cope4.nii.gz \
      sub-IPLSCI104     run2  sci   $indir/sub-IPLSCI104_run-2.feat/stats/cope4.nii.gz \
      sub-IPLSCI105     run1  sci   $indir/sub-IPLSCI105_run-1.feat/stats/cope4.nii.gz \
      sub-IPLSCI105     run2  sci   $indir/sub-IPLSCI105_run-2.feat/stats/cope4.nii.gz \

All of the required R packages seemed to be able to load without issue, but afterward, I received this error: missing value where TRUE/FALSE needed

++++++++++++++++++++++++++++++++++++++++++++++++++++
***** Summary information of data structure *****
16 response values
2 levels for factor group : hc sci

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: [-5181.417, 2601.186]

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: \u2018lmerTest\u2019

The following object is masked from \u2018package:lme4\u2019:

  lmer

The following object is masked from \u2018package:stats\u2019:

  step

Loading required package: phia
Loading required package: car
Loading required package: carData

Error in if (ii < dimx) ii <- ii + 1 else if (jj < dimy) { :
  missing value where TRUE/FALSE needed
Execution halted

I saw an user reported the same issue in this thread, but wasn't able to follow up because the topic has been closed: [afni.nimh.nih.gov]

I'm using afni 22.1.14 and R 4.0.4. The only R package that I wasn't able to install is 'brms' because there were issues installing igraph in R 4.0. Please let me know if you need any other information.

Thank you,
Tien