3dLME error

[sns]

I have tried to run a 3dLME model but got the attached error. I am trying to examine activation during levels of the task in relation to mean reaction time. The variable names in the code match the columns of the data frame, and there are no missing data in the data frame. I am not sure what could be the issue? Any insight/suggestions would be greatly appreciated.

3dLME -prefix ${output_directory}/RT_fourlevels+tlrc
-jobs 8
-model ‘StimTypemeanRTacrossrun’
-qVars “StimType,meanRTacrossrun”
-ranEff ‘~1+RT’
-num_glt 7
-SS_type 3
-gltLabel 1 ‘0back_RT’ -gltCode 1 'StimType: 10back meanRTacrossrun :’
-gltLabel 2 ‘1back_RT’ -gltCode 2 ‘StimType: 11back meanRTacrossrun :’
-gltLabel 3 ‘2back_RT’ -gltCode 3 'StimType: 12back meanRTacrossrun :’
-gltLabel 4 ‘3back_RT’ -gltCode 4 ‘StimType: 13back meanRTacrossrun :’
-gltLabel 5 ‘3v0_RT’ -gltCode 5 'StimType: 13back -10back meanRTacrossrun :’
-gltLabel 6 ‘2v0_RT’ -gltCode 6 'StimType: 12back -10back meanRTacrossrun :’
-gltLabel 7 ‘1v0_RT’ -gltCode 7 'StimType: 11back -1*0back meanRTacrossrun :’
-dataTable @DataTable_nocrosshair_withSD.txt

Data table structure:
Subj StimType meanRTacrossrun meanACCacrossrun InputFile
536 0back 616.9448 0.9732 ‘0backmap+tlrc’
536 1back X X ‘1backmap+tlrc’
…
(and the last slash in the data table has been removed)

[Gang]

It is difficult to offer specific help without understanding your data structure and analytical goal.

-ranEff ‘~1+RT’ \

You don’t have a variable “RT” in your data.

[sns]

Thanks for pointing that out. I have updated the code to include the variable name meanRTacrossruns instead of just RT.

The data is from an n-back task. For each subject, we have mean reaction time (RT) for each level of the task (0back, 1back, 2back, 3back), and a variability map for activation for each subject and level of the task. We are trying to examine the relation between within-subject variability in BOLD signal and mean RT for the different stimulus types, as well as how mean RT is associated with the difference in variability between different levels of the stimulus type factor (i.e., 3back vs. 0back).

We are thinking that the error (that still happens after updating the “RT”) is related to the data table…
Here is a larger portion of the data table:
Subj StimType meanRTacrossrun meanACCacrossrun InputFile \
1 0back 616.9448 0.9732 ‘0back_variability_map+tlrc’ \
1 1back X X ‘1back_variability_map+tlrc’
1 2back X X ‘2back_variability_map+tlrc’ \
1 3back X X ‘3back_variability_map+tlrc’ \
…
48 0back X X ‘0back_variability_map+tlrc’ \
…

But, it could be that the -ranEff or -SS_type that we have chosen are not logical with what we are trying to do? We structured our script based on example 2 on this webpage: https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dLME.html
In our data, meanRTacrossruns is a within-subject quantitative variable, and generally, the meanRTacrossruns value increases at each increasing level of the n-back task.
We believe that marginal sum of squares (the default, 3) is best, but are certainly open to suggestions.

Thanks for your help.

[Gang]

One issue is that you need to add an empty space after “StimType” in each of the following 7 lines:

-gltLabel 1 '0back_RT' -gltCode 1 'StimType: 1*0back meanRTacrossrun :' \
-gltLabel 2 '1back_RT' -gltCode 2 'StimType: 1*1back meanRTacrossrun :' \
-gltLabel 3 '2back_RT' -gltCode 3 'StimType: 1*2back meanRTacrossrun :' \
-gltLabel 4 '3back_RT' -gltCode 4 'StimType: 1*3back meanRTacrossrun :' \
-gltLabel 5 '3v0_RT' -gltCode 5 'StimType: 1*3back -1*0back meanRTacrossrun :' \
-gltLabel 6 '2v0_RT' -gltCode 6 'StimType: 1*2back -1*0back meanRTacrossrun :' \
-gltLabel 7 '1v0_RT' -gltCode 7 'StimType: 1*1back -1*0back meanRTacrossrun :' \

If you’re interested in comparing the three stimulus types (it looks like you’re not), you may need to center the RT values properly if you believe RT differs across the stimulus types.

[sns]

Thank you for pointing that out! However, the model still does not run and produces the error that essentially says:

“Make sure that packages nlme and phia are installed
Inappropriate model specification with options -model, or -qVars
Incorrect specifications in general linear test coding with -gltCode
Mistakes in data table
Inconsistent variable names that are case sensitive”

We know the the R packages are installed, and that the data table has consistent variable names and no missing values, so any suggestions about what could be going wrong with the model or glt coding would be greatly appreciated!

[Gang]

Did you have the following line in your script?

-qVars "StimType,meanRTacrossrun" \

If so, that would be troubling since ‘StimType’ is not a quantitative variable in your case.

[charujing123]

Dear AFNI experts

I have also a ‘phia’ install problems:

The OS is CentOS Linux release 7.9.2009 (Core)；
The R is R version 3.6.0 (2019-04-26) – “Planting of a Tree”
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

[root@localhost abin]# ./rPkgsInstall -pkgs ‘phia’ -update -site ‘http://cloud.r-project.org’
Installing package into ‘/root/R’
(as ‘lib’ is unspecified)
also installing the dependencies ‘curl’, ‘pbkrtest’, ‘rio’, ‘nloptr’, ‘car’, ‘lme4’

trying URL ‘http://cloud.r-project.org/src/contrib/curl_4.3.tar.gz’
Content type ‘application/x-gzip’ length 673779 bytes (657 KB)

downloaded 657 KB

trying URL ‘http://cloud.r-project.org/src/contrib/pbkrtest_0.5.1.tar.gz’
Content type ‘application/x-gzip’ length 246327 bytes (240 KB)

downloaded 240 KB

trying URL ‘http://cloud.r-project.org/src/contrib/rio_0.5.26.tar.gz’
Content type ‘application/x-gzip’ length 384305 bytes (375 KB)

downloaded 375 KB

trying URL ‘http://cloud.r-project.org/src/contrib/nloptr_1.2.2.2.tar.gz’
Content type ‘application/x-gzip’ length 2450931 bytes (2.3 MB)

downloaded 2.3 MB

trying URL ‘http://cloud.r-project.org/src/contrib/car_3.0-10.tar.gz’
Content type ‘application/x-gzip’ length 501293 bytes (489 KB)

downloaded 489 KB

trying URL ‘http://cloud.r-project.org/src/contrib/lme4_1.1-26.tar.gz’
Content type ‘application/x-gzip’ length 3297635 bytes (3.1 MB)

downloaded 3.1 MB

trying URL ‘http://cloud.r-project.org/src/contrib/phia_0.2-1.tar.gz’
Content type ‘application/x-gzip’ length 547339 bytes (534 KB)

downloaded 534 KB

• installing source package ‘curl’ …
  ** package ‘curl’ successfully unpacked and MD5 sums checked
  ** using staged installation
  Package libcurl was not found in the pkg-config search path.
  Perhaps you should add the directory containing libcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing libcurl.pc’
  to the PKG_CONFIG_PATH environment variable
  No package ‘libcurl’ found
  Using PKG_CFLAGS=
  Using PKG_LIBS=-lcurl
  ------------------------- ANTICONF ERROR ---------------------------
  Configuration failed because libcurl was not found. Try installing:
• deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
• rpm: libcurl-devel (Fedora, CentOS, RHEL)
• csw: libcurl_dev (Solaris)
  If libcurl is already installed, check that ‘pkg-config’ is in your
  PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
  is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
  R CMD INSTALL --configure-vars=‘INCLUDE_DIR=… LIB_DIR=…’

---

ERROR: configuration failed for package ‘curl’

• removing ‘/root/R/curl’
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  checking for g++ -m64 -std=gnu++11 option to produce PIC… -fPIC -DPIC
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  configure: creating ./config.status
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  config.status: creating config.h
  config.status: executing depfiles commands
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  make all-recursive
  make[1]: Entering directory /tmp/RtmpHZMqHj/R.INSTALL5ad44606040b1/nloptr/src/nlopt_src' Making all in util make[2]: Entering directory /tmp/RtmpHZMqHj/R.INSTALL5ad44606040b1/nloptr/src/nlopt_src/util’
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  libtool: compile: g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT qsort_r.lo -MD -MP -MF .deps/qsort_r.Tpo -c qsort_r.c -o qsort_r.o >/dev/null 2>&1
  mv -f .deps/qsort_r.Tpo .deps/qsort_r.Plo
  /bin/sh …/libtool --tag=CC --mode=compile g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT rescale.lo -MD -MP -MF .deps/rescale.Tpo -c -o rescale.lo rescale.c
  libtool: compile: g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT rescale.lo -MD -MP -MF .deps/rescale.Tpo -c rescale.c -fPIC -DPIC -o .libs/rescale.o
  libtool: compile: g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT rescale.lo -MD -MP -MF .deps/rescale.Tpo -c rescale.c -o rescale.o >/dev/null 2>&1
  mv -f .deps/rescale.Tpo .deps/rescale.Plo
  /bin/sh …/libtool --tag=CC --mode=link g++ -m64 -std=gnu++11 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -o libutil.la mt19937ar.lo sobolseq.lo timer.lo stop.lo redblack.lo qsort_r.lo rescale.lo -lm
  libtool: link: ERROR: no information for variable ‘AR’ cru .libs/libutil.a .libs/mt19937ar.o .libs/sobolseq.o .libs/timer.o .libs/stop.o .libs/redblack.o .libs/qsort_r.o .libs/rescale.o
  …/libtool: line 1102: ERROR:: command not found
  make[2]: *** [libutil.la] Error 127
  make[2]: Leaving directory /tmp/RtmpHZMqHj/R.INSTALL5ad44606040b1/nloptr/src/nlopt_src/util' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory /tmp/RtmpHZMqHj/R.INSTALL5ad44606040b1/nloptr/src/nlopt_src’
  make: *** [all] Error 2
  ERROR: configuration failed for package ‘nloptr’
• removing ‘/root/R/nloptr’
  ERROR: dependency ‘curl’ is not available for package ‘rio’
• removing ‘/root/R/rio’
  ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
• removing ‘/root/R/lme4’
  ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
• removing ‘/root/R/pbkrtest’
  ERROR: dependencies ‘pbkrtest’, ‘rio’, ‘lme4’ are not available for package ‘car’
• removing ‘/root/R/car’
  ERROR: dependency ‘car’ is not available for package ‘phia’
• removing ‘/root/R/phia’

The downloaded source packages are in
‘/tmp/RtmpwNBwOB/downloaded_packages’

++ Note: @ 17:21:56
This package has been installed on the computer: phia

++ Note: @ 17:21:57
This package has been updated on the computer:

Warning messages:
1: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘curl’ had non-zero exit status
2: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘nloptr’ had non-zero exit status
3: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘rio’ had non-zero exit status
4: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘lme4’ had non-zero exit status
5: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘pbkrtest’ had non-zero exit status
6: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘car’ had non-zero exit status
7: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘phia’ had non-zero exit status