3dLMEr Errors: missing value where TRUE/FALSE needed

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: https://afni.nimh.nih.gov/afni/community/board/read.php?1,162874,164369#msg-164369

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

I’m using afni 22.1.14

Tien, could you update your AFNI and see if the most recent version would fix the issue?

@update.afni.binaries -d

Thank you, Gang! And yes, updating AFNI fixed the issue.

Sorry for double posting–I meant to reply to this message.

Hello,
I was wondering if the issue from the original poster was solved? I am having the same error come up when I am using 3dLME.

We are trying to examine group by condition where group has two categories (“pos” and “neg”) and cond has two categories (“threat” and “safe”). I updated R and all AFNI binaries in Ubuntu. I have checked to ensure that there are not extra tabs or spaces in the script. I used an existing script that ran correctly (and checked that the original version ran correctly today), just modified the conditions and stats files. However when trying to run the the updated version I get this error:


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

Below is my full script and the full output.

My script (all values separated by one tab):


3dLME	-prefix	st_LME_jan11 -jobs	4	\
	-model 'Group*Cond' -mask masked+tlrc	\
	-ranEff '~1'	\
	-SS_type 3	\
	-dataTable	\
	Subj	Group	Cond	InputFile	\
	001	neg	threat	/mnt/c/TS_MID/stats.1.block+tlrc'[threat#0_Coef]'	\
	001	neg	safe	/mnt/c/TS_MID/stats.1.block+tlrc'[safe#0_Coef]'	\
	002	neg	threat	/mnt/c/TS_MID/stats.2.block+tlrc'[threat#0_Coef]'	\
	002	neg	safe	/mnt/c/TS_MID/stats.2.block+tlrc'[safe#0_Coef]'	\
	003	neg	threat	/mnt/c/TS_MID/stats.3.block+tlrc'[threat#0_Coef]'	\
	003	neg	safe	/mnt/c/TS_MID/stats.3.block+tlrc'[safe#0_Coef]'	\
	004	pos	threat	/mnt/c/TS_MID/stats.4.block+tlrc'[threat#0_Coef]'	\
	004	pos	safe	/mnt/c/TS_MID/stats.4.block+tlrc'[safe#0_Coef]'	\
	005	neg	threat	/mnt/c/TS_MID/stats.5.block+tlrc'[threat#0_Coef]'	\
	005	neg	safe	/mnt/c/TS_MID/stats.5.block+tlrc'[safe#0_Coef]'	\
	006	neg	threat	/mnt/c/TS_MID/stats.6.block+tlrc'[threat#0_Coef]'	\
	006	neg	safe	/mnt/c/TS_MID/stats.6.block+tlrc'[safe#0_Coef]'	\
	007	pos	threat	/mnt/c/TS_MID/stats.7.block+tlrc'[threat#0_Coef]'	\
	007	pos	safe	/mnt/c/TS_MID/stats.7.block+tlrc'[safe#0_Coef]'	\
	008	neg	threat	/mnt/c/TS_MID/stats.8.block+tlrc'[threat#0_Coef]'	\
	008	neg	safe	/mnt/c/TS_MID/stats.8.block+tlrc'[safe#0_Coef]'	\
	009	pos	threat	/mnt/c/TS_MID/stats.9.block+tlrc'[threat#0_Coef]'	\
	009	pos	safe	/mnt/c/TS_MID/stats.9.block+tlrc'[safe#0_Coef]'	\
	010	neg	threat	/mnt/c/TS_MID/stats.10.block+tlrc'[threat#0_Coef]'	\
	010	neg	safe	/mnt/c/TS_MID/stats.10.block+tlrc'[safe#0_Coef]'	\
	011	neg	threat	/mnt/c/TS_MID/stats.11.block+tlrc'[threat#0_Coef]'	\
	011	neg	safe	/mnt/c/TS_MID/stats.11.block+tlrc'[safe#0_Coef]'	\
	012	pos	threat	/mnt/c/TS_MID/stats.12.block+tlrc'[threat#0_Coef]'	\
	012	pos	safe	/mnt/c/TS_MID/stats.12.block+tlrc'[safe#0_Coef]'	\
	013	neg	threat	/mnt/c/TS_MID/stats.13.block+tlrc'[threat#0_Coef]'	\
	013	neg	safe	/mnt/c/TS_MID/stats.13.block+tlrc'[safe#0_Coef]'	\
	014	neg	threat	/mnt/c/TS_MID/stats.14.block+tlrc'[threat#0_Coef]'	\
	014	neg	safe	/mnt/c/TS_MID/stats.14.block+tlrc'[safe#0_Coef]'	\
	015	neg	threat	/mnt/c/TS_MID/stats.15.block+tlrc'[threat#0_Coef]'	\
	015	neg	safe	/mnt/c/TS_MID/stats.15.block+tlrc'[safe#0_Coef]'	\
	016	neg	threat	/mnt/c/TS_MID/stats.16.block+tlrc'[threat#0_Coef]'	\
	016	neg	safe	/mnt/c/TS_MID/stats.16.block+tlrc'[safe#0_Coef]'	\
	017	pos	threat	/mnt/c/TS_MID/stats.17.block+tlrc'[threat#0_Coef]'	\
	017	pos	safe	/mnt/c/TS_MID/stats.17.block+tlrc'[safe#0_Coef]'	\
	018	neg	threat	/mnt/c/TS_MID/stats.18.block+tlrc'[threat#0_Coef]'	\
	018	neg	safe	/mnt/c/TS_MID/stats.18.block+tlrc'[safe#0_Coef]'	\
	019	neg	threat	/mnt/c/TS_MID/stats.19.block+tlrc'[threat#0_Coef]'	\
	019	neg	safe	/mnt/c/TS_MID/stats.19.block+tlrc'[safe#0_Coef]'	\
	020	pos	threat	/mnt/c/TS_MID/stats.20.block+tlrc'[threat#0_Coef]'	\
	020	pos	safe	/mnt/c/TS_MID/stats.20.block+tlrc'[safe#0_Coef]'	\
	021	neg	threat	/mnt/c/TS_MID/stats.21.block+tlrc'[threat#0_Coef]'	\
	021	neg	safe	/mnt/c/TS_MID/stats.21.block+tlrc'[safe#0_Coef]'	\
	022	pos	threat	/mnt/c/TS_MID/stats.22.block+tlrc'[threat#0_Coef]'	\
	022	pos	safe	/mnt/c/TS_MID/stats.22.block+tlrc'[safe#0_Coef]'	\
	023	pos	threat	/mnt/c/TS_MID/stats.23.block+tlrc'[threat#0_Coef]'	\
	023	pos	safe	/mnt/c/TS_MID/stats.23.block+tlrc'[safe#0_Coef]'	\
	024	neg	threat	/mnt/c/TS_MID/stats.24.block+tlrc'[threat#0_Coef]'	\
	024	neg	safe	/mnt/c/TS_MID/stats.24.block+tlrc'[safe#0_Coef]'	\
	028	pos	threat	/mnt/c/TS_MID/stats.28.block+tlrc'[threat#0_Coef]'	\
	028	pos	safe	/mnt/c/TS_MID/stats.28.block+tlrc'[safe#0_Coef]'	\
	029	pos	threat	/mnt/c/TS_MID/stats.29.block+tlrc'[threat#0_Coef]'	\
	029	pos	safe	/mnt/c/TS_MID/stats.29.block+tlrc'[safe#0_Coef]'	\
	031	pos	threat	/mnt/c/TS_MID/stats.31.block+tlrc'[threat#0_Coef]'	\
	031	pos	safe	/mnt/c/TS_MID/stats.31.block+tlrc'[safe#0_Coef]'	\
	033	pos	threat	/mnt/c/TS_MID/stats.33.block+tlrc'[threat#0_Coef]'	\
	033	pos	safe	/mnt/c/TS_MID/stats.33.block+tlrc'[safe#0_Coef]'	\
	034	pos	threat	/mnt/c/TS_MID/stats.34.block+tlrc'[threat#0_Coef]'	\
	034	pos	safe	/mnt/c/TS_MID/stats.34.block+tlrc'[safe#0_Coef]'	\
	035	pos	threat	/mnt/c/TS_MID/stats.35.block+tlrc'[threat#0_Coef]'	\
	035	pos	safe	/mnt/c/TS_MID/stats.35.block+tlrc'[safe#0_Coef]'	\
	038	pos	threat	/mnt/c/TS_MID/stats.38.block+tlrc'[threat#0_Coef]'	\
	038	pos	safe	/mnt/c/TS_MID/stats.38.block+tlrc'[safe#0_Coef]'	\
	039	pos	threat	/mnt/c/TS_MID/stats.39.block+tlrc'[threat#0_Coef]'	\
	039	pos	safe	/mnt/c/TS_MID/stats.39.block+tlrc'[safe#0_Coef]'	\
	040	neg	threat	/mnt/c/TS_MID/stats.40.block+tlrc'[threat#0_Coef]'	\
	040	neg	safe	/mnt/c/TS_MID/stats.40.block+tlrc'[safe#0_Coef]'	\
	041	pos	threat	/mnt/c/TS_MID/stats.41.block+tlrc'[threat#0_Coef]'	\
	041	pos	safe	/mnt/c/TS_MID/stats.41.block+tlrc'[safe#0_Coef]'	\
	042	neg	threat	/mnt/c/TS_MID/stats.42.block+tlrc'[threat#0_Coef]'	\
	042	neg	safe	/mnt/c/TS_MID/stats.42.block+tlrc'[safe#0_Coef]'	\
	043	neg	threat	/mnt/c/TS_MID/stats.43.block+tlrc'[threat#0_Coef]'	\
	043	neg	safe	/mnt/c/TS_MID/stats.43.block+tlrc'[safe#0_Coef]'	\
	044	neg	threat	/mnt/c/TS_MID/stats.44.block+tlrc'[threat#0_Coef]'	\
	044	neg	safe	/mnt/c/TS_MID/stats.44.block+tlrc'[safe#0_Coef]'	\
	045	neg	threat	/mnt/c/TS_MID/stats.45.block+tlrc'[threat#0_Coef]'	\
	045	neg	safe	/mnt/c/TS_MID/stats.45.block+tlrc'[safe#0_Coef]'	\
	046	neg	threat	/mnt/c/TS_MID/stats.46.block+tlrc'[threat#0_Coef]'	\
	046	neg	safe	/mnt/c/TS_MID/stats.46.block+tlrc'[safe#0_Coef]'	\
	047	neg	threat	/mnt/c/TS_MID/stats.47.block+tlrc'[threat#0_Coef]'	\
	047	neg	safe	/mnt/c/TS_MID/stats.47.block+tlrc'[safe#0_Coef]'	\
	048	neg	threat	/mnt/c/TS_MID/stats.48.block+tlrc'[threat#0_Coef]'	\
	048	neg	safe	/mnt/c/TS_MID/stats.48.block+tlrc'[safe#0_Coef]'	\
	049	neg	threat	/mnt/c/TS_MID/stats.49.block+tlrc'[threat#0_Coef]'	\
	049	neg	safe	/mnt/c/TS_MID/stats.49.block+tlrc'[safe#0_Coef]'	\
	050	neg	threat	/mnt/c/TS_MID/stats.50.block+tlrc'[threat#0_Coef]'	\
	050	neg	safe	/mnt/c/TS_MID/stats.50.block+tlrc'[safe#0_Coef]'	\
	051	pos	threat	/mnt/c/TS_MID/stats.51.block+tlrc'[threat#0_Coef]'	\
	051	pos	safe	/mnt/c/TS_MID/stats.51.block+tlrc'[safe#0_Coef]'	\
	052	pos	threat	/mnt/c/TS_MID/stats.52.block+tlrc'[threat#0_Coef]'	\
	052	pos	safe	/mnt/c/TS_MID/stats.52.block+tlrc'[safe#0_Coef]'	\
	053	neg	threat	/mnt/c/TS_MID/stats.53.block+tlrc'[threat#0_Coef]'	\
	053	neg	safe	/mnt/c/TS_MID/stats.53.block+tlrc'[safe#0_Coef]'	\
	054	pos	threat	/mnt/c/TS_MID/stats.54.block+tlrc'[threat#0_Coef]'	\
	054	pos	safe	/mnt/c/TS_MID/stats.54.block+tlrc'[safe#0_Coef]'	\
	055	neg	threat	/mnt/c/TS_MID/stats.55.block+tlrc'[threat#0_Coef]'	\
	055	neg	safe	/mnt/c/TS_MID/stats.55.block+tlrc'[safe#0_Coef]'	\
	056	pos	threat	/mnt/c/TS_MID/stats.56.block+tlrc'[threat#0_Coef]'	\
	056	pos	safe	/mnt/c/TS_MID/stats.56.block+tlrc'[safe#0_Coef]'	\
	057	neg	threat	/mnt/c/TS_MID/stats.57.block+tlrc'[threat#0_Coef]'	\
	057	neg	safe	/mnt/c/TS_MID/stats.57.block+tlrc'[safe#0_Coef]'	\
	058	neg	threat	/mnt/c/TS_MID/stats.58.block+tlrc'[threat#0_Coef]'	\
	058	neg	safe	/mnt/c/TS_MID/stats.58.block+tlrc'[safe#0_Coef]'	\
	059	neg	threat	/mnt/c/TS_MID/stats.59.block+tlrc'[threat#0_Coef]'	\
	059	neg	safe	/mnt/c/TS_MID/stats.59.block+tlrc'[safe#0_Coef]'	\
	060	pos	threat	/mnt/c/TS_MID/stats.60.block+tlrc'[threat#0_Coef]'	\
	060	pos	safe	/mnt/c/TS_MID/stats.60.block+tlrc'[safe#0_Coef]'	\
	061	neg	threat	/mnt/c/TS_MID/stats.61.block+tlrc'[threat#0_Coef]'	\
	061	neg	safe	/mnt/c/TS_MID/stats.61.block+tlrc'[safe#0_Coef]'	\
	062	pos	threat	/mnt/c/TS_MID/stats.62.block+tlrc'[threat#0_Coef]'	\
	062	pos	safe	/mnt/c/TS_MID/stats.62.block+tlrc'[safe#0_Coef]'	\
	063	neg	threat	/mnt/c/TS_MID/stats.63.block+tlrc'[threat#0_Coef]'	\
	063	neg	safe	/mnt/c/TS_MID/stats.63.block+tlrc'[safe#0_Coef]'	\
	064	pos	threat	/mnt/c/TS_MID/stats.64.block+tlrc'[threat#0_Coef]'	\
	064	pos	safe	/mnt/c/TS_MID/stats.64.block+tlrc'[safe#0_Coef]'	\
	065	neg	threat	/mnt/c/TS_MID/stats.65.block+tlrc'[threat#0_Coef]'	\
	065	neg	safe	/mnt/c/TS_MID/stats.65.block+tlrc'[safe#0_Coef]'	\
	066	neg	threat	/mnt/c/TS_MID/stats.66.block+tlrc'[threat#0_Coef]'	\
	066	neg	safe	/mnt/c/TS_MID/stats.66.block+tlrc'[safe#0_Coef]'	\
	067	pos	threat	/mnt/c/TS_MID/stats.67.block+tlrc'[threat#0_Coef]'	\
	067	pos	safe	/mnt/c/TS_MID/stats.67.block+tlrc'[safe#0_Coef]'	\
	068	pos	threat	/mnt/c/TS_MID/stats.68.block+tlrc'[threat#0_Coef]'	\
	068	pos	safe	/mnt/c/TS_MID/stats.68.block+tlrc'[safe#0_Coef]'	\
	069	neg	threat	/mnt/c/TS_MID/stats.69.block+tlrc'[threat#0_Coef]'	\
	069	neg	safe	/mnt/c/TS_MID/stats.69.block+tlrc'[safe#0_Coef]'	\
	070	neg	threat	/mnt/c/TS_MID/stats.70.block+tlrc'[threat#0_Coef]'	\
	070	neg	safe	/mnt/c/TS_MID/stats.70.block+tlrc'[safe#0_Coef]'	\
	071	neg	threat	/mnt/c/TS_MID/stats.71.block+tlrc'[threat#0_Coef]'	\
	071	neg	safe	/mnt/c/TS_MID/stats.71.block+tlrc'[safe#0_Coef]'	\
	072	pos	threat	/mnt/c/TS_MID/stats.72.block+tlrc'[threat#0_Coef]'	\
	072	pos	safe	/mnt/c/TS_MID/stats.72.block+tlrc'[safe#0_Coef]'	\
	073	neg	threat	/mnt/c/TS_MID/stats.73.block+tlrc'[threat#0_Coef]'	\
	073	neg	safe	/mnt/c/TS_MID/stats.73.block+tlrc'[safe#0_Coef]'	\
	077	neg	threat	/mnt/c/TS_MID/stats.77.block+tlrc'[threat#0_Coef]'	\
	077	neg	safe	/mnt/c/TS_MID/stats.77.block+tlrc'[safe#0_Coef]'	\
	078	pos	threat	/mnt/c/TS_MID/stats.78.block+tlrc'[threat#0_Coef]'	\
	078	pos	safe	/mnt/c/TS_MID/stats.78.block+tlrc'[safe#0_Coef]'	\
	079	pos	threat	/mnt/c/TS_MID/stats.79.block+tlrc'[threat#0_Coef]'	\
	079	pos	safe	/mnt/c/TS_MID/stats.79.block+tlrc'[safe#0_Coef]'	\
	080	neg	threat	/mnt/c/TS_MID/stats.80.block+tlrc'[threat#0_Coef]'	\
	080	neg	safe	/mnt/c/TS_MID/stats.80.block+tlrc'[safe#0_Coef]'	\
	081	neg	threat	/mnt/c/TS_MID/stats.81.block+tlrc'[threat#0_Coef]'	\
	081	neg	safe	/mnt/c/TS_MID/stats.81.block+tlrc'[safe#0_Coef]'	\
	082	pos	threat	/mnt/c/TS_MID/stats.82.block+tlrc'[threat#0_Coef]'	\
	082	pos	safe	/mnt/c/TS_MID/stats.82.block+tlrc'[safe#0_Coef]'	\
	083	neg	threat	/mnt/c/TS_MID/stats.83.block+tlrc'[threat#0_Coef]'	\
	083	neg	safe	/mnt/c/TS_MID/stats.83.block+tlrc'[safe#0_Coef]'	\
	084	pos	threat	/mnt/c/TS_MID/stats.84.block+tlrc'[threat#0_Coef]'	\
	084	pos	safe	/mnt/c/TS_MID/stats.84.block+tlrc'[safe#0_Coef]'	\
	085	neg	threat	/mnt/c/TS_MID/stats.85.block+tlrc'[threat#0_Coef]'	\
	085	neg	safe	/mnt/c/TS_MID/stats.85.block+tlrc'[safe#0_Coef]'

This is the output (with the error at the end)


/mnt/c/TS_MID$ tcsh safethreat_LME_jan11
Loading required package: nlme
Package nlme loaded successfully!

Loading required package: phia
Loading required package: car
Loading required package: carData
Package phia loaded successfully!


++++++++++++++++++++++++++++++++++++++++++++++++++++
***** Summary information of data structure *****
75 subjects :  001 002 003 004 005 006 007 008 009 010 011 012 013 014 015 016 017 018 019 020 021 022 023 024 028 029 031 033 034 035 038 039 040 041 042 043 044 045 046 047 048 049 050 051 052 053 054 055 056 057 058 059 060 061 062 063 064 065 066 067 068 069 070 071 072 073 077 078 079 080 081 082 083 084 085
150 response values
2 levels for factor Group : neg pos
2 levels for factor Cond : safe threat
0 post hoc tests

Contingency tables of subject distributions among the categorical variables:


Tabulation of subjects against all categorical variables
~~~~~~~~~~~~~~
Subj vs Group:

      neg pos
  001   2   0
  002   2   0
  003   2   0
  004   0   2
  005   2   0
  006   2   0
  007   0   2
  008   2   0
  009   0   2
  010   2   0
  011   2   0
  012   0   2
  013   2   0
  014   2   0
  015   2   0
  016   2   0
  017   0   2
  018   2   0
  019   2   0
  020   0   2
  021   2   0
  022   0   2
  023   0   2
  024   2   0
  028   0   2
  029   0   2
  031   0   2
  033   0   2
  034   0   2
  035   0   2
  038   0   2
  039   0   2
  040   2   0
  041   0   2
  042   2   0
  043   2   0
  044   2   0
  045   2   0
  046   2   0
  047   2   0
  048   2   0
  049   2   0
  050   2   0
  051   0   2
  052   0   2
  053   2   0
  054   0   2
  055   2   0
  056   0   2
  057   2   0
  058   2   0
  059   2   0
  060   0   2
  061   2   0
  062   0   2
  063   2   0
  064   0   2
  065   2   0
  066   2   0
  067   0   2
  068   0   2
  069   2   0
  070   2   0
  071   2   0
  072   0   2
  073   2   0
  077   2   0
  078   0   2
  079   0   2
  080   2   0
  081   2   0
  082   0   2
  083   2   0
  084   0   2
  085   2   0

~~~~~~~~~~~~~~
Subj vs Cond:

      safe threat
  001    1      1
  002    1      1
  003    1      1
  004    1      1
  005    1      1
  006    1      1
  007    1      1
  008    1      1
  009    1      1
  010    1      1
  011    1      1
  012    1      1
  013    1      1
  014    1      1
  015    1      1
  016    1      1
  017    1      1
  018    1      1
  019    1      1
  020    1      1
  021    1      1
  022    1      1
  023    1      1
  024    1      1
  028    1      1
  029    1      1
  031    1      1
  033    1      1
  034    1      1
  035    1      1
  038    1      1
  039    1      1
  040    1      1
  041    1      1
  042    1      1
  043    1      1
  044    1      1
  045    1      1
  046    1      1
  047    1      1
  048    1      1
  049    1      1
  050    1      1
  051    1      1
  052    1      1
  053    1      1
  054    1      1
  055    1      1
  056    1      1
  057    1      1
  058    1      1
  059    1      1
  060    1      1
  061    1      1
  062    1      1
  063    1      1
  064    1      1
  065    1      1
  066    1      1
  067    1      1
  068    1      1
  069    1      1
  070    1      1
  071    1      1
  072    1      1
  073    1      1
  077    1      1
  078    1      1
  079    1      1
  080    1      1
  081    1      1
  082    1      1
  083    1      1
  084    1      1
  085    1      1
***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++

Reading input files now...

Reading input files: Done!


Range of input data: [-13.914, 17.730]

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

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

Any help with this would be greatly appreciated!

Thank you,
Kate

What is your AFNI version?

afni -ver

Consider updating your AFNI:

@update.afni.binaries -d

and try running 3dLME again.

Hi Gang,
I updated AFNI yesterday when the issue first occured. I tried to update it again today per your suggestions and it says no update need. I am currently running Version AFNI_23.0.00 ‘Commodus’. I tried the 3dLME again just now and I got the same error.

Thanks to Gang, I was able to fix the issue. The mask I was using in AFNI contained nonzero values so the mask was not recognized. I converted the original file to a recognizable mask with


3dcalc -a masked+tlrc. -expr 'step(a)' -prefix myMask

Thanks again Gang!