Thank you very much for that information. I think I was able to figure out what I needed to include in my final script. I have been trying to run a test version of my script (just on 3 subjects and without the glfs) for awhile and finally got it to read the input files. However, now I am receiving this error: Model Test Failed. Here is the output. Any thoughts about how to proceed? I also put the script below as well.

Package nlme loaded successfully!

Package phia loaded successfully!


++++++++++++++++++++++++++++++++++++++++++++++++++++
***** Summary information of data structure *****
3 subjects : 102_day1 104_day1 109_day1
12 response values
2 levels for factor Valence : neg neu
2 levels for factor Predict : p u
12 centered values for numeric variable Age : 17.36667 17.36667 17.36667 17.36667 -7.133333 -7.133333 -7.133333 -7.133333 -10.23333 -10.23333 -10.23333 -10.23333
2 levels for factor Sex : 0 1
12 centered values for numeric variable PCL5 : -17.66667 -17.66667 -17.66667 -17.66667 3.333333 3.333333 3.333333 3.333333 14.33333 14.33333 14.33333 14.33333
14 post hoc tests

Contingency tables of subject distributions among the categorical variables:


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

neg neu
102_day1 2 2
104_day1 2 2
109_day1 2 2

~~~~~~~~~~~~~~
Subj vs Predict:

p u
102_day1 2 2
104_day1 2 2
109_day1 2 2

~~~~~~~~~~~~~~
Subj vs Sex:

0 1
102_day1 4 0
104_day1 0 4
109_day1 0 4
***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++

Reading input files now...

Reading input files: Done!

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.

~~~~~~~~~~~~~~~~~~~ Model test failed ~~~~~~~~~~~~~~~~~~~
Possible reasons:

0) Make sure that R packages nlme and phia have been installed. See the 3dLME
help documentation for more details.

1) Inappropriate model specification with options -model, or -qVars.

2) In correct specifications in general linear test coding with -gltCode.

3) Mistakes in data table. Check the data structure shown above, and verify
whether there are any inconsistencies.

4) Inconsistent variable names which are case sensitive. For example, factor
named Group in model specification and then listed as group in the table hader
would cause grief for 3dLME.


#!/bin/tcsh
module load pkgsrc/2018Q3
module load pkgsrc/gcc-base
module load /sharedapps/LS/psych_imaging/modulefiles/afni/08.28.2017
3dLME -prefix unc_cl_test -jobs 6 \
-model "Valence*Predict*PCL5+Age+Sex" \
-qVars "Age,PCL5" \
-ranEff "~1+Age" \
-SS_type 3 \
-num_glt 14 \
-gltLabel 1 'neg-neu' -gltCode 1 'Valence : 1*neg -1*neu' \
-gltLabel 2 'u-p' -gltCode 2 'Predict : 1*u -1*p' \
-gltLabel 3 'Uneg-Uneu' -gltCode 3 'Valence : 1*neg -1*neu Predict : 1*u' \
-gltLabel 4 'Pneg-Pneu' -gltCode 4 'Valence : 1*neg -1*neu Predict : 1*p' \
-gltLabel 5 'Uneg-Pneg' -gltCode 5 'Predict : 1*u -1*p Valence : 1*neg' \
-gltLabel 6 'Uneu-Pneu' -gltCode 6 'Predict : 1*u -1*p Valence : 1*neu' \
-gltLabel 7 'Uneg-Pneu' -gltCode 7 'Predict : 1*u -1*p Valence : 1*neg -1*neu' \
-gltLabel 8 'neg-neu_PCL5' -gltCode 8 'Valence : 1*neg -1*neu PCL5 :' \
-gltLabel 9 'u-p_PCL5' -gltCode 9 'Predict : 1*u -1*p PCL5 :' \
-gltLabel 10 'Uneg-Uneu_PCL5' -gltCode 10 'Valence : 1*neg -1*neu Predict : 1*u PCL5 :' \
-gltLabel 11 'Pneg-Pneu_PCL5' -gltCode 11 'Valence : 1*neg -1*neu Predict : 1*p PCL5 :' \
-gltLabel 12 'Uneg-Pneg_PCL5' -gltCode 12 'Predict : 1*u -1*p Valence : 1*neg PCL5 :' \
-gltLabel 13 'Uneu-Pneu_PCL5' -gltCode 13 'Predict : 1*u -1*p Valence : 1*neu PCL5 :' \
-gltLabel 14 'Uneg-Pneu_PCL5' -gltCode 14 'Predict : 1*u -1*p Valence : 1*neg -1*neu PCL5 :' \
-dataTable \
Subj Valence Predict Age Sex PCL5 InputFile \
102_day1 neg p 49.3 0 14 102_day1/unc_trl_results/peak/Pneg_cl+tlrc \
102_day1 neu p 49.3 0 14 102_day1/unc_trl_results/peak/Pneu_cl+tlrc \
102_day1 neg u 49.3 0 14 102_day1/unc_trl_results/peak/Uneg_cl+tlrc \
102_day1 neu u 49.3 0 14 102_day1/unc_trl_results/peak/Uneu_cl+tlrc \
104_day1 neg p 24.8 1 35 104_day1/unc_trl_results/peak/Pneg_cl+tlrc \
104_day1 neu p 24.8 1 35 104_day1/unc_trl_results/peak/Pneu_cl+tlrc \
104_day1 neg u 24.8 1 35 104_day1/unc_trl_results/peak/Uneg_cl+tlrc \
104_day1 neu u 24.8 1 35 104_day1/unc_trl_results/peak/Uneu_cl+tlrc \
109_day1 neg p 21.7 1 46 109_day1/unc_trl_results/peak/Pneg_cl+tlrc \
109_day1 neu p 21.7 1 46 109_day1/unc_trl_results/peak/Pneu_cl+tlrc \
109_day1 neg u 21.7 1 46 109_day1/unc_trl_results/peak/Uneg_cl+tlrc \
109_day1 neu u 21.7 1 46 109_day1/unc_trl_results/peak/Uneu_cl+tlrc