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 'time*group+FD+acc+age+sex+(1|Subj)' \
-qVars 'FD,acc,age' \
-gltCode pre 'time:1*pre' \
-gltCode post-pre 'time : 1*post -1*pre' \
-gltCode ar_post-pre 'time : 1*post -1*pre group : 1*ar' \
-gltCode hc_post-pre 'time : 1*post -1*pre group : 1*hc' \
-gltCode ar-hc_post-pre 'time : 1*post -1*pre group : 1*ar -1*hc' \
-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!
