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Liu Mengxing
September 25, 2015 10:11AM
Dear AFNI developers:

I was trying to do 3dLME, but the error kept coming,here are the stdout:
[Macmini:~] liumengxing%: csh /Users/liumengxing/Desktop/group_ancova.sh
Loading required package: nlme
Package nlme loaded successfully!

Loading required package: phia
Loading required package: car
Package phia loaded successfully!


++++++++++++++++++++++++++++++++++++++++++++++++++++
***** Summary information of data structure *****
62 subjects : sub01 sub02 sub03 sub04 sub05 sub06 sub07 sub08 sub09 sub10 sub11 sub12 sub13 sub14 sub15 sub16 sub17 sub18 sub19 sub20 sub21 sub22 sub23 sub24 sub25 sub26 sub27 sub28 sub29 sub30 sub31 sub32 sub33 sub34 sub35 sub36 sub37 sub38 sub39 sub40 sub41 sub42 sub43 sub44 sub45 sub46 sub47 sub48 sub49 sub50 sub51 sub52 sub53 sub54 sub55 sub56 sub57 sub58 sub59 sub60 sub61 sub62
62 response values
2 levels for factor Task : Listen Reading
2 levels for factor Lang : Chn Eng
15 post hoc tests

Contingency tables of subject distributions among the categorical variables:

Lang
Task Chn Eng
Listen 16 15
Reading 16 15

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

Listen Reading
sub01 1 0
sub02 1 0
sub03 1 0
sub04 1 0
sub05 1 0
sub06 1 0
sub07 1 0
sub08 1 0
sub09 1 0
sub10 1 0
sub11 1 0
sub12 1 0
sub13 1 0
sub14 1 0
sub15 1 0
sub16 1 0
sub17 0 1
sub18 0 1
sub19 0 1
sub20 0 1
sub21 0 1
sub22 0 1
sub23 0 1
sub24 0 1
sub25 0 1
sub26 0 1
sub27 0 1
sub28 0 1
sub29 0 1
sub30 0 1
sub31 0 1
sub32 0 1
sub33 1 0
sub34 1 0
sub35 1 0
sub36 1 0
sub37 1 0
sub38 1 0
sub39 1 0
sub40 1 0
sub41 1 0
sub42 1 0
sub43 1 0
sub44 1 0
sub45 1 0
sub46 1 0
sub47 1 0
sub48 0 1
sub49 0 1
sub50 0 1
sub51 0 1
sub52 0 1
sub53 0 1
sub54 0 1
sub55 0 1
sub56 0 1
sub57 0 1
sub58 0 1
sub59 0 1
sub60 0 1
sub61 0 1
sub62 0 1

~~~~~~~~~~~~~~
Subj vs Lang:

Chn Eng
sub01 1 0
sub02 1 0
sub03 1 0
sub04 1 0
sub05 1 0
sub06 1 0
sub07 1 0
sub08 1 0
sub09 1 0
sub10 1 0
sub11 1 0
sub12 1 0
sub13 1 0
sub14 1 0
sub15 1 0
sub16 1 0
sub17 1 0
sub18 1 0
sub19 1 0
sub20 1 0
sub21 1 0
sub22 1 0
sub23 1 0
sub24 1 0
sub25 1 0
sub26 1 0
sub27 1 0
sub28 1 0
sub29 1 0
sub30 1 0
sub31 1 0
sub32 1 0
sub33 0 1
sub34 0 1
sub35 0 1
sub36 0 1
sub37 0 1
sub38 0 1
sub39 0 1
sub40 0 1
sub41 0 1
sub42 0 1
sub43 0 1
sub44 0 1
sub45 0 1
sub46 0 1
sub47 0 1
sub48 0 1
sub49 0 1
sub50 0 1
sub51 0 1
sub52 0 1
sub53 0 1
sub54 0 1
sub55 0 1
sub56 0 1
sub57 0 1
sub58 0 1
sub59 0 1
sub60 0 1
sub61 0 1
sub62 0 1
***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++

Reading input files now...

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.

Error in if (is.na(lop$gltList[[n]])) gltRes[[n]] <- tryCatch(testInteractions(fm, :
argument is of length zero
Execution halted
Loading required package: nlme
Package nlme loaded successfully!

Loading required package: phia
Loading required package: car
Package phia loaded successfully!


++++++++++++++++++++++++++++++++++++++++++++++++++++
***** Summary information of data structure *****
62 subjects : sub01 sub02 sub03 sub04 sub05 sub06 sub07 sub08 sub09 sub10 sub11 sub12 sub13 sub14 sub15 sub16 sub17 sub18 sub19 sub20 sub21 sub22 sub23 sub24 sub25 sub26 sub27 sub28 sub29 sub30 sub31 sub32 sub33 sub34 sub35 sub36 sub37 sub38 sub39 sub40 sub41 sub42 sub43 sub44 sub45 sub46 sub47 sub48 sub49 sub50 sub51 sub52 sub53 sub54 sub55 sub56 sub57 sub58 sub59 sub60 sub61 sub62
62 response values
2 levels for factor Task : Listen Reading
2 levels for factor Lang : Chn Eng
15 post hoc tests

Contingency tables of subject distributions among the categorical variables:

Lang
Task Chn Eng
Listen 16 15
Reading 16 15

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

Listen Reading
sub01 1 0
sub02 1 0
sub03 1 0
sub04 1 0
sub05 1 0
sub06 1 0
sub07 1 0
sub08 1 0
sub09 1 0
sub10 1 0
sub11 1 0
sub12 1 0
sub13 1 0
sub14 1 0
sub15 1 0
sub16 1 0
sub17 0 1
sub18 0 1
sub19 0 1
sub20 0 1
sub21 0 1
sub22 0 1
sub23 0 1
sub24 0 1
sub25 0 1
sub26 0 1
sub27 0 1
sub28 0 1
sub29 0 1
sub30 0 1
sub31 0 1
sub32 0 1
sub33 1 0
sub34 1 0
sub35 1 0
sub36 1 0
sub37 1 0
sub38 1 0
sub39 1 0
sub40 1 0
sub41 1 0
sub42 1 0
sub43 1 0
sub44 1 0
sub45 1 0
sub46 1 0
sub47 1 0
sub48 0 1
sub49 0 1
sub50 0 1
sub51 0 1
sub52 0 1
sub53 0 1
sub54 0 1
sub55 0 1
sub56 0 1
sub57 0 1
sub58 0 1
sub59 0 1
sub60 0 1
sub61 0 1
sub62 0 1

~~~~~~~~~~~~~~
Subj vs Lang:

Chn Eng
sub01 1 0
sub02 1 0
sub03 1 0
sub04 1 0
sub05 1 0
sub06 1 0
sub07 1 0
sub08 1 0
sub09 1 0
sub10 1 0
sub11 1 0
sub12 1 0
sub13 1 0
sub14 1 0
sub15 1 0
sub16 1 0
sub17 1 0
sub18 1 0
sub19 1 0
sub20 1 0
sub21 1 0
sub22 1 0
sub23 1 0
sub24 1 0
sub25 1 0
sub26 1 0
sub27 1 0
sub28 1 0
sub29 1 0
sub30 1 0
sub31 1 0
sub32 1 0
sub33 0 1
sub34 0 1
sub35 0 1
sub36 0 1
sub37 0 1
sub38 0 1
sub39 0 1
sub40 0 1
sub41 0 1
sub42 0 1
sub43 0 1
sub44 0 1
sub45 0 1
sub46 0 1
sub47 0 1
sub48 0 1
sub49 0 1
sub50 0 1
sub51 0 1
sub52 0 1
sub53 0 1
sub54 0 1
sub55 0 1
sub56 0 1
sub57 0 1
sub58 0 1
sub59 0 1
sub60 0 1
sub61 0 1
sub62 0 1
***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++

Reading input files now...

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.

Error in if (is.na(lop$gltList[[n]])) gltRes[[n]] <- tryCatch(testInteractions(fm, :
argument is of length zero
Execution halted



Below is my script:
#!/bin/csh
set chn="/Users/liumengxing/Research/story/chinese/analysis"
set eng="/Users/liumengxing/Research/story/english/analysis"
set spath="/Users/liumengxing/Research/story"
cd "$spath"/ANOVA2/
foreach hemi (lh rh)
3dLME -prefix "$hemi"_ANCOVA \
-jobs 4 -model "Task*Lang" \
-ranEff '~1' -SS_type 3 \
-num_glt 15 \
-gltLabel 1 Task -gltCode 1 'Task: 1*Listen - 1*Reading' \
-gltLabel 2 Lang -gltCode 2 'Lang: 1*Chn - 1*Eng' \
-gltLabel 3 TaskByLang -gltCode 3 'Task: 1*Listen - 1*Reading Lang: 1*Chn - 1*Eng' \
-gltLabel 4 Lis_Chn-Eng -gltCode 4 'Lang: 1*Chn - 1*Eng Task: 1*Listen' \
-gltLabel 5 Rea_Chn-Eng -gltCode 5 'Lang: 1*Chn - 1*Eng Task: 1*Reading' \
-gltLabel 6 Chn_Lis-Rea -gltCode 6 'Task: 1*Listen - 1*Reading Lang: 1*Chn' \
-gltLabel 7 Eng_Lis-Rea -gltCode 7 'Task: 1*Listen - 1*Reading Lang: 1*Eng' \
-gltLabel 8 Listen -gltCode 8 'Task: 1*Listen' \
-gltLabel 9 Reading -gltCode 9 'Task: 1*Reading' \
-gltLabel 10 Chinese -gltCode 10 'Lang: 1*Chn' \
-gltLabel 11 English -gltCode 11 'Lang: 1*Eng' \
-gltLabel 12 Lis_Chn -gltCode 12 'Task: 1*Listen Lang: 1*Chn' \
-gltLabel 13 Lis_Eng -gltCode 13 'Task: 1*Listen Lang: 1*Eng' \
-gltLabel 14 Rea_Chn -gltCode 14 'Task: 1*Reading Lang: 1*Chn' \
-gltLabel 15 Rea_Eng -gltCode 15 'Task: 1*Reading Lang: 1*Eng' \
-dataTable \
Subj Task Lang InputFile \
sub01 Listen Chn "$chn"/sub01/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub02 Listen Chn "$chn"/sub02/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub03 Listen Chn "$chn"/sub03/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub04 Listen Chn "$chn"/sub04/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub05 Listen Chn "$chn"/sub05/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub06 Listen Chn "$chn"/sub06/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub07 Listen Chn "$chn"/sub07/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub08 Listen Chn "$chn"/sub08/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub09 Listen Chn "$chn"/sub09/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub10 Listen Chn "$chn"/sub10/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub11 Listen Chn "$chn"/sub11/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub12 Listen Chn "$chn"/sub12/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub13 Listen Chn "$chn"/sub13/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub14 Listen Chn "$chn"/sub14/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub15 Listen Chn "$chn"/sub15/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub16 Listen Chn "$chn"/sub16/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub17 Reading Chn "$chn"/sub01/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub18 Reading Chn "$chn"/sub02/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub19 Reading Chn "$chn"/sub03/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub20 Reading Chn "$chn"/sub04/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub21 Reading Chn "$chn"/sub05/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub22 Reading Chn "$chn"/sub06/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub23 Reading Chn "$chn"/sub07/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub24 Reading Chn "$chn"/sub08/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub25 Reading Chn "$chn"/sub09/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub26 Reading Chn "$chn"/sub10/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub27 Reading Chn "$chn"/sub11/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub28 Reading Chn "$chn"/sub12/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub29 Reading Chn "$chn"/sub13/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub30 Reading Chn "$chn"/sub14/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub31 Reading Chn "$chn"/sub15/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub32 Reading Chn "$chn"/sub16/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub33 Listen Eng "$eng"/sub01/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub34 Listen Eng "$eng"/sub02/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub35 Listen Eng "$eng"/sub03/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub36 Listen Eng "$eng"/sub04/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub37 Listen Eng "$eng"/sub05/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub38 Listen Eng "$eng"/sub06/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub39 Listen Eng "$eng"/sub07/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub40 Listen Eng "$eng"/sub09/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub41 Listen Eng "$eng"/sub10/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub42 Listen Eng "$eng"/sub11/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub43 Listen Eng "$eng"/sub13/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub44 Listen Eng "$eng"/sub14/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub45 Listen Eng "$eng"/sub15/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub46 Listen Eng "$eng"/sub16/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub47 Listen Eng "$eng"/sub17/surface_files/"$hemi"_GLM_glts.1D\[8] \
sub48 Reading Eng "$eng"/sub01/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub49 Reading Eng "$eng"/sub02/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub50 Reading Eng "$eng"/sub03/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub51 Reading Eng "$eng"/sub04/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub52 Reading Eng "$eng"/sub05/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub53 Reading Eng "$eng"/sub06/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub54 Reading Eng "$eng"/sub07/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub55 Reading Eng "$eng"/sub09/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub56 Reading Eng "$eng"/sub10/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub57 Reading Eng "$eng"/sub11/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub58 Reading Eng "$eng"/sub13/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub59 Reading Eng "$eng"/sub14/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub60 Reading Eng "$eng"/sub15/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub61 Reading Eng "$eng"/sub16/surface_files/"$hemi"_GLM_glts.1D\[10] \
sub62 Reading Eng "$eng"/sub17/surface_files/"$hemi"_GLM_glts.1D\[10]
end

AFNI version:Precompiled binary macosx_10.7_Intel_64: Nov 19 2014 (Version AFNI_2011_12_21_1014)
I do want to use the latest version of AFNI, but it doesn't work well with R, so I chose 10.7
R version:R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)


plantform: Macmini OS X 10.10.5



Edited 1 time(s). Last edit at 09/25/2015 11:17AM by Liu Mengxing.
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Subject Author Posted

Erro in 3dLME

Liu Mengxing September 25, 2015 10:11AM

Re: Erro in 3dLME

gang September 25, 2015 12:35PM

Re: Erro in 3dLME

Liu Mengxing September 25, 2015 08:00PM

Re: Erro in 3dLME

gang September 25, 2015 09:21PM

Re: Erro in 3dLME

Liu Mengxing September 25, 2015 09:40PM

Re: Erro in 3dLME

gang September 28, 2015 01:14PM

Re: Erro in 3dLME

Liu Mengxing September 28, 2015 09:10PM