3dLMEr error

I am trying to run 3dLMEr to assess group*time interaction effects in an n-back task in an intervention vs. control group. (I am using 3dLMEr because I have within-subject quantitative covariates - FD and accuracy - that I would like to adjust for.) I previously had 3dLME up and running on another environment, but I have R 4.0.3 on this workstation, so it has been a challenge. I updated all of the afni binaries, environment is Ubuntu 18.04. I am running the following script:

3dLMEr -prefix 3dLMEr_210108 -jobs 8
-model ‘timegroup+FD+acc+age+sex+(1|Subj)’
-qVars ‘FD,acc,age’
-gltCode pre 'time:1
pre’
-gltCode post-pre ‘time : 1post -1pre’
-gltCode ar_post-pre ‘time : 1post -1pre group : 1ar’
-gltCode hc_post-pre 'time : 1
post -1pre group : 1hc’
-gltCode ar-hc_post-pre ‘time : 1post -1pre group : 1ar -1hc’
-dataTable
Subj time group FD acc age sex InputFile
109 pre ar 0.3092 1.8772 12.5689 2 ./sub-109/ses-pre/sub-109_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
109 post ar 0.326 1.9745 12.8892 2 ./sub-109/ses-post/sub-109_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
110 pre ar 0.2643 1.9808 13.8558 1 ./sub-110/ses-pre/sub-110_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
110 post ar 0.2576 2.3835 14.0885 1 ./sub-110/ses-post/sub-110_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
119 pre ar 0.1286 2.9635 11.5095 2 ./sub-119/ses-pre/sub-119_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
119 post ar 0.1158 3.0864 11.9092 2 ./sub-119/ses-post/sub-119_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
124 pre ar 0.1311 1.2896 10.3239 1 ./sub-124/ses-pre/sub-124_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
124 post ar 0.1519 1.813 10.7236 1 ./sub-124/ses-post/sub-124_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
127 pre ar 0.2883 3.7359 10.3841 1 ./sub-127/ses-pre/sub-127_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
127 post ar 0.3291 2.9461 10.7072 1 ./sub-127/ses-post/sub-127_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
128 pre ar 0.2272 3.7942 11.1015 1 ./sub-128/ses-pre/sub-128_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
128 post ar 0.1256 3.178 11.4246 1 ./sub-128/ses-post/sub-128_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
129 pre ar 0.2199 2.7887 14.2582 1 ./sub-129/ses-pre/sub-129_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
129 post ar 0.1458 3.7359 14.4744 1 ./sub-129/ses-post/sub-129_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
130 pre ar 0.2279 2.9461 13.1549 2 ./sub-130/ses-pre/sub-130_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
130 post ar 0.1995 3.0864 13.363 2 ./sub-130/ses-post/sub-130_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
136 pre ar 0.2367 3.178 13.311 1 ./sub-136/ses-pre/sub-136_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
136 post ar 0.2914 4.1753 13.7518 1 ./sub-136/ses-post/sub-136_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
138 pre ar 0.193 2.7221 10.8112 2 ./sub-138/ses-pre/sub-138_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
138 post ar 0.4512 3.3182 11.2109 2 ./sub-138/ses-post/sub-138_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
203 pre hc 0.2172 2.2184 14.4443 1 ./sub-203/ses-pre/sub-203_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
203 post hc 0.1747 3.3384 14.5922 1 ./sub-203/ses-post/sub-203_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
205 pre hc 0.1807 4.1753 13.2535 2 ./sub-205/ses-pre/sub-205_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
205 post hc 0.1835 4.1917 13.4643 2 ./sub-205/ses-post/sub-205_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
209 pre hc 0.3255 2.9132 14.5675 1 ./sub-209/ses-pre/sub-209_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
209 post hc 0.2085 3.4982 14.7564 1 ./sub-209/ses-post/sub-209_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
210 pre hc 0.1665 2.0478 12.8483 2 ./sub-210/ses-pre/sub-210_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
210 post hc 0.1973 1.4666 13.0098 2 ./sub-210/ses-post/sub-210_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
211 pre hc 0.0875 3.3182 13.0399 2 ./sub-211/ses-pre/sub-211_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
211 post hc 0.1077 4.6311 13.2343 2 ./sub-211/ses-post/sub-211_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
217 pre hc 0.178 3.4931 10.6524 1 ./sub-217/ses-pre/sub-217_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
217 post hc 0.1132 3.6174 10.8495 1 ./sub-217/ses-post/sub-217_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
218 pre hc 0.1415 2.9825 11.3753 2 ./sub-218/ses-pre/sub-218_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
218 post hc 0.1694 3.9598 11.5368 2 ./sub-218/ses-post/sub-218_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
220 pre hc 0.2591 1.5738 11.3534 2 ./sub-220/ses-pre/sub-220_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
220 post hc 0.2951 3.7576 11.5423 2 ./sub-220/ses-post/sub-220_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
222 pre hc 0.1961 3.0955 12.662 2 ./sub-222/ses-pre/sub-222_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
222 post hc 0.1428 3.0955 12.662 2 ./sub-222/ses-post/sub-222_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
225 pre hc 0.0968 1.3492 12.0405 1 ./sub-225/ses-pre/sub-225_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
225 post hc 0.209 1.6906 12.2239 1 ./sub-225/ses-post/sub-225_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
226 pre hc 0.1721 3.3182 10.8825 1 ./sub-226/ses-pre/sub-226_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
226 post hc 0.2322 3.3182 11.1645 1 ./sub-226/ses-post/sub-226_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
227 pre hc 0.1739 4.1917 13.1439 2 ./sub-227/ses-pre/sub-227_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
227 post hc 0.3218 3.0955 13.3903 2 ./sub-227/ses-post/sub-227_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
228 pre hc 0.1159 3.2612 13.6477 2 ./sub-228/ses-pre/sub-228_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
228 post hc 0.1358 4.1917 13.7764 2 ./sub-228/ses-post/sub-228_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
229 pre hc 0.2671 2.6154 11.849 2 ./sub-229/ses-pre/sub-229_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
229 post hc 0.2855 3.7359 12.1063 2 ./sub-229/ses-post/sub-229_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
230 pre hc 0.0715 4.1753 14.8933 1 ./sub-230/ses-pre/sub-230_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
230 post hc 0.167 2.3426 15.1069 1 ./sub-230/ses-post/sub-230_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
231 pre hc 0.2402 2.9132 12.8619 2 ./sub-231/ses-pre/sub-231_ses-pre_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’
231 post hc 0.2037 3.2119 13.0508 2 ./sub-231/ses-post/sub-231_ses-post_reml+tlrc’[TwoBack-ZeroBack#0_Coef]’

When I run this, I get the following error:
Error in [.data.frame(dataStr, , vars[ii]) : undefined columns selected
Calls: process.LME.opts … gl_Constr → glfConstr → levels → [ → [.data.frame
Execution halted

I thought I would make things simple and delete the contrasts (i.e. the -gltCode lines) for now, which then gives me the following error:
** Error:
Missing librio.so
Error in if (an$type == “BRIK” && !is.na(an$view)) { :
missing value where TRUE/FALSE needed
Calls: process.LME.opts → exists.AFNI.name → file.exists → head.AFNI.name
Execution halted

I thought I would try with tabs instead of spaces in the dataframe and that changes the error to:
Error in if (len%%wd != 0) errex.AFNI(paste(“The content under -dataTable is not rectangular!”, :
argument is of length zero
Calls: process.LME.opts
Execution halted

I have checked each version of these programs using file_tool and there are no problems. This is also my first time conducting first-level analysis in AFNI, so I am not 100% sure I have entered the file names correctly? I am also not sure if it has something to do with the installation. Any advice would be much appreciated! Thank you!

Not so sure about the other two errors, but you need to add an empty space after ‘time’ and before “1*pre”:

-gltCode pre ‘time:1*pre’ \

which should be

-gltCode pre ‘time : 1*pre’ \

See how it goes once you fix this.

This indeed solves the first error - thank you for that! And now I am left with the other two. I am not sure if these are related to installation of AFNI and version of R? When I installed AFNI, I already had two versions of R on my workstation, one that I use regularly (R 4.0.3 in /usr/bin/R) and another one (R 3.6.3 in /opt/R/3.6.3/bin/R). I assumed AFNI was using the R in my path (which R=/usr/bin/R), but when I run the command lines to install R (i.e.sudo tcsh @add_rcran_ubuntu_18.04.tcsh), I get the following message:

+* Warning! Existing R version detected:

   R version 3.6.3 (2020-02-29)

** If you still want to carry on with this installation,
you MUST use the following option with this command:
-overwrite
If you have any questions, please ask on the AFNI Message
Board.

I would rather not overwrite my current version of R (4.0.3) with an earlier version, so I have not yet tried this option. I don’t know if it will be necessary for AFNI installation, and if this has anything to do with the error message that I am getting? (or if it is much simpler than that??) Thanks in advance for your help!