3dLME dataTable issue

AFNI Message Board
1

Dear AFNI team,

I am having some issue of running 3dLME, and it seems to be the dataTable error:
"Read 70 items
Error in [.data.frame(dataStr, , vars[ii]) : undefined columns selected
Calls: process.LME.opts ... gl_Constr -> glfConstr -> levels -> [ -> [.data.frame
Execution halted"

Here is my code:

3dLME -prefix NKI_LMM \
      -jobs 9 \
      -model "age+sex+TIV+race" \
      -ranEff "~1+Subj" \
      -SS_type 3 \
      -qVars "age,TIV" \
      -qVarCenters "0,1474.114" \
      -mask /home/zxwang/projects/2023/sex_diff/NKI_AFNI_Test/data/MNI152_T1_brainmask_1.5mm.nii.gz \
      -num_glt 4 \
      -num_glf 1 \
      -gltLabel 1 'Age' -gltCode 1 'age' \
      -gltLabel 2 'Sex' -gltCode 2 'sex' \
      -gltLabel 3 'TIV' -gltCode 3 'TIV' \
      -gltLabel 4 'Race' -gltCode 4 'race' \
      -glfLabel 1 'Global Test' -glfCode 1 'age+sex+TIV+race' \
      -dataTable @AFNI_data_table_10.txt

I am testing the age, sex, total brain volume effects of my data, I'll attach my AFNI_data_table_10.txt below:

Subj	intercept	age	sex	TIV	race	InputFile
37	1	-6.286115007	1	1482.952776	1	/home/NKI_AFNI_Test/data/smwp1rsub-A00040117_ses-BAS1_T1w.nii
37	1	-4.286115007	1	1504.352244	1	/home/NKI_AFNI_Test/data/smwp1rsub-A00040117_ses-FLU1_T1w.nii
37	1	-3.286115007	1	1523.376345	1	/home/NKI_AFNI_Test/data/smwp1rsub-A00040117_ses-FLU2_T1w.nii
230	1	-4.286115007	1	1401.461332	1	/home/NKI_AFNI_Test/data/smwp1rsub-A00062349_ses-FLU2_T1w.nii
230	1	-4.286115007	1	1407.272761	1	/home/NKI_AFNI_Test/data/smwp1rsub-A00062349_ses-TRT_T1w.nii
193	1	-6.286115007	0	1369.313943	1	/home/NKI_AFNI_Test/data/smwp1rsub-A00055832_ses-BAS1_T1w.nii
193	1	-5.286115007	0	1403.403798	1	/home/NKI_AFNI_Test/data/smwp1rsub-A00055832_ses-FLU1_T1w.nii
102	1	-6.286115007	1	1570.168817	0	/home/NKI_AFNI_Test/data/smwp1rsub-A00081842_ses-BAS1_T1w.nii
102	1	-5.286115007	1	1583.480603	0	/home/NKI_AFNI_Test/data/smwp1rsub-A00081842_ses-FLU1_T1w.nii

I didn't find any issue that could cause undefined selected columns. Would you mind letting me know the issue that could cause this error?

Thank you!

Zexi

2

There are a couple of issues with the 3dLME specifications:

(1) If this is a longitudinal study, consider using the following specification:

-ranEff "~1+age" \

(2) The specifications using -gltCode and -glfCode are not correct. I recommend referring to the 3dLME help documentation and examples for the proper usage.

Gang