[picchionid@cn4292 test_10.02.07_no_cond_in_model]$ afni -ver
Precompiled binary linux_rocky_8: Sep 18 2024 (Version AFNI_24.2.07 'Macrinus')
[picchionid@cn4292 test_10.02.07_no_cond_in_model]$ R --version
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Gang!
Hi! How are you? The revisions to our sleep manuscript are going well. I have a question for you.
I ran a 3dLMEr command successfully. Great results. Perfect. Replicates prior work. Already robust against many exploratory tweaks of the analysis. It used the quantitative factor of auditory arousal threshold (AAT). This quantitative factor comes from a sound pressure level meter where the firmware automatically performs a log() transformation because that is very standard. The team and I wanted to check whether the results are further robust against using the nontransformed values, so I repeated the command with a 10^AAT transformation. When I did so, 3dLMEr gave me "Error: Quitting due to model test failure." Why might that happen? See below for the successful version of the code and the output from 3dLMEr from unsuccessful code.
Sincerely,
Dante
Excerpt from successful code:
3dLMEr \
-prefix output_lme_audaro_hip_procbasic_rz_nocondinmodel.nii \
-jobs 32 \
-model "1+AAT+(1+AAT|Subj)" \
-qVars 'AAT' \
-R2 \
-SS_type 3 \
-gltCode AATeff 'AAT : ' \
-dataTable \
Subj Noise Cond AAT SStage InputFile \
s00003 0.924046 aro1 70 n3 ../20160713_2255_hip_procbasic_rz.nii
s00003 0.593909 aro2 25 n2 ../20160713_2326_hip_procbasic_rz.nii
...
s00105 0.0916635 aro5 0 r ../20170413_0535_hip_procbasic_rz.nii
Output from 3dLMEr from unsuccessful code:
Dimensions:
rows: 77 | columns: 6
+* Warning: Each "Subj" does not have the same number of "InputFiles"!
Most Subj have 8 InputFiles. The following Subj differ:
Subj NumInputFiles
s00003 5
s00014 6
s00047 5
s00056 7
s00060 4
s00063 6
s00086 7
s00105 5
Data summary:
Variable Detected_Type Details
Subj Subjects Num Subjects=12
Noise Quantitative Min=0.0155511 | Max=0.990234
Cond Categorical Unique levels=8
AAT Quantitative Min=1 | Max=1e+70 | Num outliers=17
SStage Categorical Unique levels=5
InputFile Data Number of InputFiles=77
++ Good: All InputFiles exist.
++ Good: All InputFiles have exactly 1 volume.
++ Good: All InputFiles are on the same grid.
++++++++++++++++++++++++++++++++++++++++++++++++++++
***** Summary information of data structure *****
77 response values
8 levels for factor Cond : aro1 aro2 aro3 aro4 aro5 aro6 aro7 aro8
77 centered values for numeric variable AAT : 9.74026e+69 -2.597403e+68 -2.597403e+68 -2.597403e+68 9.74026e+69 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68 -2.597403e+68
5 levels for factor SStage : n1 n2 n3 r w
***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++
Reading input files now...
Reading input files for effect estimates: Done!
Range of input data: [-1.406, 1.716]
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: lme4
Loading required package: Matrix
Package lme4 loaded successfully!
Loading required package: lmerTest
Attaching package: ‘lmerTest’
The following object is masked from ‘package:lme4’:
lmer
The following object is masked from ‘package:stats’:
step
Package lmerTest loaded successfully!
Loading required package: phia
Loading required package: car
Loading required package: carData
Package phia loaded successfully!
Loading required package: MuMIn
Package MuMIn loaded successfully!
~~~~~~~~~~~~~~~~~~~ Model test failed ~~~~~~~~~~~~~~~~~~~
Possible reasons:
0) Missing R packages lme4, lmerTest, and phia.
1) Inappropriate model specification with options -model, or -qVars.
2) Incorrect specifications with -gltCode.
3) inconsistencies in the data table.
4) Inconsistent variable names (e.g., typos, case sensitive characters).
** Error:
Quitting due to model test failure...