New program 3dLMEr for linear mixed-effects modeling

aojha17 · September 18, 2020, 11:32pm

Hi Gang,

Thanks for the reply! I’m still having some trouble (“model test failed”). I’m working with a miniature version of the final script for debugging purposes, posted here:

3dLMEr -prefix EFNBACK_LMER_mini2 -jobs 12
-model ‘emotiongroup+site(1|Subj)’
-bounds -2 2
-gltCode p-d 'group : 1p -1d emotion : 1pos’
-gltCode p-d ‘group : 1p emotion : 1pos -1*neg’
-dataTable
Subj emotion group site InputFile
95008 pos p TRIO 2pos-nopic_95008+tlrc.
95008 neg p TRIO 2neg-nopic_95008+tlrc.
95012 pos d TRIO 2pos-nopic_95012+tlrc.
95012 neg d TRIO 2neg-nopic_95012+tlrc.
91003 pos d PRISMA2 2pos-nopic_91003+tlrc.
91003 neg d PRISMA2 2neg-nopic_91003+tlrc.

Thanks in advance!
Amar

Gang · September 22, 2020, 12:31am

Amar, the problem with this miniature version is that the number of subjects is too small to be identifiable for the model. In addition, you may need to use different labels for the two specifications:

-gltCode p-d ‘group : 1p -1d emotion : 1pos’
-gltCode p-d 'group : 1p emotion : 1pos -1neg’ \

aojha17 · September 22, 2020, 7:41pm

Hi Gang,

I’m now getting an error that says “object ‘xinit’ not found”—I installed “lmerTest,” “snow,” and “phia.” I see someone else had the same problem but don’t see a solution to it. I didn’t see ‘xinit’ in the 3dLMEr script itself but did in the 3dLMERr.R script… Any help, as always, is greatly appreciated!

Amar

Gang · September 22, 2020, 8:00pm

Are you using a mask? If so, perform the analysis without the mask and you can apply the mask afterward on the output.

aojha17 · September 23, 2020, 1:01am

Hi Gang,

That got rid of the error regarding ‘xinit’ but I’m still getting the earlier error that the model test failed, despite now including everyone and using different label specifications. I’m including the full script below. Thank you for your help!!

Amar

3dLMEr -prefix 3DLMER_EFNBACK -jobs 12
#-mask EmoVNeu_Thresh_resamp_binary.nii
-model ‘emotiongroup+site(1|Subj)’
-bounds -2 2
-gltCode p-d_pos 'group : 1p -1d emotion : 1pos’
-gltCode p-d_neg ‘group : 1p -1d emotion : 1neg’
-gltCode p-d_neut 'group : 1p -1d emotion : 1neut’
-gltCode p-na_pos ‘group : 1p -1na emotion : 1pos’
-gltCode p-na_neg 'group : 1p -1na emotion : 1neg’
-gltCode p-na_neut ‘group : 1p -1na emotion : 1neut’
-gltCode d-na_pos 'group : 1d -1na emotion : 1pos’
-gltCode d-na_neg ‘group : 1d -1na emotion : 1neg’
-gltCode d-na_neut 'group : 1d -1na emotion : 1neut’
-gltCode pos-neg_p ‘group : 1p emotion : 1pos -1neut’
-gltCode pos-neg_d 'group : 1d emotion : 1pos -1neut’
-gltCode pos-neg_na ‘group : 1na emotion : 1pos -1neut’
-gltCode pos-neg_p 'group : 1p emotion : 1neg -1neut’
-gltCode pos-neg_d ‘group : 1d emotion : 1neg -1neut’
-gltCode pos-neg_na 'group : 1na emotion : 1neg -1neut’
-gltCode pos-neg_p ‘group : 1p emotion : 1pos -1neg’
-gltCode pos-neg_d 'group : 1d emotion : 1pos -1neg’
-gltCode pos-neg_na ‘group : 1na emotion : 1pos -1*neg’
-dataTable @table.txt

here’s table.txt (in a shortened form here but the real one is a bit longer):

Subj site sex group age emotion InputFile
95086 PRISMA2 m d 38.69 pos 2pos-nopic_95086+tlrc.
96023 PRISMA2 m d 31.06 pos 2pos-nopic_96023+tlrc.
99004 PRISMA2 m na 37.77 pos 2pos-nopic_99004+tlrc.
99011 PRISMA2 m na 38.08 pos 2pos-nopic_99011+tlrc.
99021 PRISMA2 f na 39.06 pos 2pos-nopic_99021+tlrc.
99240 PRISMA2 m na 35.31 pos 2pos-nopic_99240+tlrc.
99248 PRISMA2 m na 41.20 pos 2pos-nopic_99248+tlrc.
99250 PRISMA2 m na 38.57 pos 2pos-nopic_99250+tlrc.
99252 PRISMA2 m na 35.72 pos 2pos-nopic_99252+tlrc.
99257 PRISMA2 m na 35.86 pos 2pos-nopic_99257+tlrc.
99262 PRISMA2 m na 34.97 pos 2pos-nopic_99262+tlrc.
99263 PRISMA2 m na 34.85 pos 2pos-nopic_99263+tlrc.
87022 PRISMA2 m d 38.61 neg 2neg-nopic_87022+tlrc
88015 PRISMA2 m p 41.60 neg 2neg-nopic_88015+tlrc
88082 PRISMA2 m d 39.46 neg 2neg-nopic_88082+tlrc
88083 PRISMA2 m p 43.92 neg 2neg-nopic_88083+tlrc
89019 PRISMA2 m d 39.11 neg 2neg-nopic_89019+tlrc
89023 PRISMA2 m p 34.03 neg 2neg-nopic_89023+tlrc
89031 PRISMA2 f p 38.36 neg 2neg-nopic_89031+tlrc
89061 PRISMA2 m d 34.59 neg 2neg-nopic_89061+tlrc
89065 PRISMA2 m d 36.82 neg 2neg-nopic_89065+tlrc
89073 PRISMA2 m p 38.79 neg 2neg-nopic_89073+tlrc
90032 PRISMA2 m d 40.62 neg 2neg-nopic_90032+tlrc
90043 PRISMA2 m d 39.35 neg 2neg-nopic_90043+tlrc
90070 PRISMA2 m p 38.11 neg 2neg-nopic_90070+tlrc
91003 PRISMA2 m d 36.76 neg 2neg-nopic_91003+tlrc
91008 PRISMA2 m p 35.90 neg 2neg-nopic_91008+tlrc
91015 PRISMA2 m d 38.86 neg 2neg-nopic_91015+tlrc
91028 PRISMA2 m d 37.61 neg 2neg-nopic_91028+tlrc
91030 PRISMA2 m p 38.43 neg 2neg-nopic_91030+tlrc
91078 PRISMA2 m d 40.10 neg 2neg-nopic_91078+tlrc
91087 PRISMA2 m d 36.42 neg 2neg-nopic_91087+tlrc
92041 PRISMA2 m d 34.50 neg 2neg-nopic_92041+tlrc
93100 PRISMA2 m p 35.87 neg 2neg-nopic_93100+tlrc
93105 PRISMA2 m d 31.11 neg 2neg-nopic_93105+tlrc
93128 PRISMA2 m p 32.84 neg 2neg-nopic_93128+tlrc
93142 PRISMA2 m d 34.54 neg 2neg-nopic_93142+tlrc
93183 PRISMA2 f d 32.83 neg 2neg-nopic_93183+tlrc
94208 PRISMA2 m d 31.58 neg 2neg-nopic_94208+tlrc
94215 PRISMA2 m p 31.21 neg 2neg-nopic_94215+tlrc
94229 PRISMA2 m d 32.12 neg 2neg-nopic_94229+tlrc
94262 PRISMA2 m p 36.23 neg 2neg-nopic_94262+tlrc
94264 PRISMA2 m d 33.12 neg 2neg-nopic_94264+tlrc
94270 PRISMA2 m d 35.44 neg 2neg-nopic_94270+tlrc
94271 PRISMA2 m d 34.44 neg 2neg-nopic_94271+tlrc
94294 PRISMA2 f p 38.55 neg 2neg-nopic_94294+tlrc
95019 PRISMA2 m p 31.93 neg 2neg-nopic_95019+tlrc
95054 PRISMA2 m d 32.30 neg 2neg-nopic_95054+tlrc
95068 PRISMA2 m d 35.39 neg 2neg-nopic_95068+tlrc
95071 PRISMA2 m d 34.64 neg 2neg-nopic_95071+tlrc
95077 PRISMA2 m d 37.09 neg 2neg-nopic_95077+tlrc
95085 PRISMA2 m d 38.90 neg 2neg-nopic_95085+tlrc
95086 PRISMA2 m d 38.69 neg 2neg-nopic_95086+tlrc
96023 PRISMA2 m d 31.06 neg 2neg-nopic_96023+tlrc
95091 TRIO m d 38.66 neg 2neg-nopic_95091+tlrc.
96011 TRIO m p 27.06 neg 2neg-nopic_96011+tlrc.
94213 TRIO m d 33.67 neut 2neut-nopic_94213+tlrc.
94230 TRIO m d 33.70 neut 2neut-nopic_94230+tlrc.
94234 TRIO m p 29.50 neut 2neut-nopic_94234+tlrc.
94237 TRIO m p 34.15 neut 2neut-nopic_94237+tlrc.
94239 TRIO m d 29.16 neut 2neut-nopic_94239+tlrc.
94244 TRIO m p 29.71 neut 2neut-nopic_94244+tlrc.
94246 TRIO m d 33.17 neut 2neut-nopic_94246+tlrc.
94248 TRIO m d 29.94 neut 2neut-nopic_94248+tlrc.
94257 TRIO m p 32.53 neut 2neut-nopic_94257+tlrc.
94301 TRIO m d 30.21 neut 2neut-nopic_94301+tlrc.
95003 TRIO m d 27.50 neut 2neut-nopic_95003+tlrc.
95008 TRIO m p 27.27 neut 2neut-nopic_95008+tlrc.
95012 TRIO f d 29.50 neut 2neut-nopic_95012+tlrc.
95015 TRIO m d 29.88 neut 2neut-nopic_95015+tlrc.
95018 TRIO m p 29.18 neut 2neut-nopic_95018+tlrc.
95070 TRIO f p 33.26 neut 2neut-nopic_95070+tlrc.
95083 TRIO f d 38.00 neut 2neut-nopic_95083+tlrc.
95088 TRIO m d 37.44 neut 2neut-nopic_95088+tlrc.
95091 TRIO m d 38.66 neut 2neut-nopic_95091+tlrc.
96011 TRIO m p 27.06 neut 2neut-nopic_96011+tlrc.
96020 TRIO m p 29.86 neut 2neut-nopic_96020+tlrc.
96033 TRIO m d 30.42 neut 2neut-nopic_96033+tlrc.
99012 TRIO m na 35.20 neut 2neut-nopic_99012+tlrc.
99016 TRIO m na 35.13 neut 2neut-nopic_99016+tlrc.
99024 TRIO m na 34.91 neut 2neut-nopic_99024+tlrc.
99032 TRIO m na 34.63 neut 2neut-nopic_99032+tlrc.
99043 TRIO f na 34.66 neut 2neut-nopic_99043+tlrc.
99045 TRIO m na 29.98 neut 2neut-nopic_99045+tlrc.
99056 TRIO m na 34.96 neut 2neut-nopic_99056+tlrc.
99062 TRIO m na 35.02 neut 2neut-nopic_99062+tlrc.
99063 TRIO m na 34.66 neut 2neut-nopic_99063+tlrc.
99080 TRIO m na 27.38 neut 2neut-nopic_99080+tlrc.
99083 TRIO m na 29.79 neut 2neut-nopic_99083+tlrc.
99092 TRIO m na 27.28 neut 2neut-nopic_99092+tlrc.
99093 TRIO m na 29.53 neut 2neut-nopic_99093+tlrc.
99110 TRIO m na 30.18 neut 2neut-nopic_99110+tlrc.
99113 TRIO m na 29.80 neut 2neut-nopic_99113+tlrc.
99117 TRIO m na 27.43 neut 2neut-nopic_99117+tlrc.
99129 TRIO m na 29.95 neut 2neut-nopic_99129+tlrc.
99147 TRIO m na 27.81 neut 2neut-nopic_99147+tlrc.
99164 TRIO m na 29.68 neut 2neut-nopic_99164+tlrc.
99167 TRIO m na 29.83 neut 2neut-nopic_99167+tlrc.
99171 TRIO m na 29.23 neut 2neut-nopic_99171+tlrc.
99172 TRIO m na 34.97 neut 2neut-nopic_99172+tlrc.
99177 TRIO f na 27.78 neut 2neut-nopic_99177+tlrc.
99192 TRIO m na 34.60 neut 2neut-nopic_99192+tlrc.
99217 TRIO m na 29.45 neut 2neut-nopic_99217+tlrc.
99221 TRIO m na 34.64 neut 2neut-nopic_99221+tlrc.
99226 TRIO m na 40.48 neut 2neut-nopic_99226+tlrc.
99228 TRIO m na 26.63 neut 2neut-nopic_99228+tlrc.
99230 TRIO m na 35.33 neut 2neut-nopic_99230+tlrc.
99231 TRIO m na 34.64 neut 2neut-nopic_99231+tlrc.
99260 TRIO m na 29.87 neut 2neut-nopic_99260+tlrc.

Gang · September 23, 2020, 2:09pm

One problem is your model specification:

-model ‘emotion*group+site(1|Subj)’ \

You likely meant to have:

-model ‘emotion*group+site+(1|Subj)’ \

aojha17 · September 23, 2020, 3:21pm

Hi Gang,

Thanks for bearing with me. Here’s a new error when I fixed the model specification:

Error in checkForRemoteErrors(val) :
11 nodes produced errors; first error: missing value where TRUE/FALSE needed
Calls: aperm … clusterApply → staticClusterApply → checkForRemoteErrors
Execution halted

Amar

henrybrice · October 20, 2020, 1:06pm

I’m getting an error trying to run 3dLMEr, on MacOs 10.15.6, afni version AFNI_20.2.16 ‘Aulus Vitellius’


Error in xinit : object 'xinit' not found

I saw this referenced in this question: https://afni.nimh.nih.gov/afni/community/board/read.php?1,164159,164159#msg-164159
But the solution offered there, namely creating an .Rprofile file in the home directory with the line ‘xinit = “NA”’ didn’t help.

Edit: The solution offered here: https://afni.nimh.nih.gov/afni/community/board/read.php?1,164763,164783#msg-164783
namely installing an earlier version of data.table, didn’t solve this either.

Gang · October 20, 2020, 4:31pm

One possible issue is that AFNI currently does not support R version 3.6.x yet. What is the output of the following command?

afni_system_check.py -check_all

henrybrice · October 20, 2020, 7:22pm


-------------------------------- general ---------------------------------
architecture:         64bit 
system:               Darwin
release:              19.6.0
version:              Darwin Kernel Version 19.6.0: Thu Jun 18 20:49:00 PDT 2020; root:xnu-6153.141.1~1/RELEASE_X86_64
distribution:         unknown Darwin
number of CPUs:       4
apparent login shell: bash
shell RC file:        .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /Users/LanguageLab/abin/afni
afni version         : Precompiled binary macos_10.12_local: Sep  1 2020 
                     : AFNI_20.2.16 'Aulus Vitellius'
AFNI_version.txt     : AFNI_20.2.16, macos_10.12_local, Sep 01 2020
which python         : /usr/local/bin/python
python version       : 2.7.15
which R              : /usr/local/bin/R
R version            : R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
which tcsh           : /bin/tcsh

instances of various programs found in PATH:
    afni    : 1   (/Users/LanguageLab/abin/afni)
    R       : 1   (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
    python  : 2 
      /usr/local/Cellar/python@2/2.7.15_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7
      /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
    python2 : 2 
      /usr/local/Cellar/python@2/2.7.15_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7
      /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
    python3 : 2 
      /usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/bin/python3.7
      /usr/bin/python3


testing ability to start various programs...
    afni                 : success
    suma                 : success
    3dSkullStrip         : success
    uber_subject.py      : success
    3dAllineate          : success
    3dRSFC               : success
    SurfMesh             : success
    3dClustSim           : success
    3dMVM                : success

checking for R packages...
    rPkgsInstall -pkgs ALL -check : success

R RHOME : /Library/Frameworks/R.framework/Resources

checking for $HOME files...
    .afnirc                   : found
    .sumarc                   : found
    .afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
++ module loaded: PyQt4
   module file : /usr/local/lib/python2.7/site-packages/PyQt4/__init__.pyc

** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable

-- python binaries under /usr/local/bin:
    /usr/local/bin/python (sym link to /usr/local/Cellar/python@2/2.7.15_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
    /usr/local/bin/python3 (sym link to /usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
    /usr/local/bin/python2 (sym link to /usr/local/Cellar/python@2/2.7.15_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
    /usr/local/bin/python3.7 (sym link to /usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
    /usr/local/bin/python2.7 (sym link to /usr/local/Cellar/python@2/2.7.15_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7)

-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/LanguageLab/abin:/Users/LanguageLab/abin

PYTHONPATH = 
R_LIBS = 
LD_LIBRARY_PATH = 
DYLD_LIBRARY_PATH = 
DYLD_FALLBACK_LIBRARY_PATH = 

------------------------------ data checks -------------------------------
data dir : found AFNI_data6   under $HOME
           top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos   under $HOME
           top history: 22 Oct 2019 [discoraj]: added Cluster Explorer Demo
data dir : found suma_demo    under $HOME
           top history: ...s_New/data/Build_tmp on Mon Mar  4 11:56:45 EST 2013
data dir : found afni_handouts under $HOME
atlas    : found TT_N27+tlrc  under /Users/LanguageLab/abin

------------------------------ OS specific -------------------------------
XQuartz version      : 2.7.11

which brew           : /usr/local/bin/brew
brew version         : Homebrew 1.6.9-111-g15ac935

++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
   -- found 'libXt' dylib files:
      /opt/X11/lib/flat_namespace/libXt.6.dylib
** env var DYLD_LIBRARY_PATH is not set to contain /opt/X11/lib/flat_namespace
   (so afni and suma may fail)

=========================  summary, please fix:  =========================
*  just be aware: login shell 'bash', but our code examples use 'tcsh'
*  OS X version might be old
*  consider setting DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace

Gang · October 21, 2020, 1:05am

Your R version might be the issue. AFNI currently does not support 3.6.x yet. Try removing R, and install the older version 3.6.3. See if that fixes the problem.

henrybrice · October 21, 2020, 9:43am

Do you mean 3.3.3?