Thank you for your quick reply, Peter.

Here is the full command and output: (I tried to examine condition*group interaction: 2 groups with ag and ctr; 2 conditions, repeated, with r1 and r2), and input files are resting-state fMRI dataset. I was puzzled when I saw the output file/image, which looks (is) the group mask. Thank you! Sophia

sh -x 3dLME.txt
+ 3dLME -prefix DBD_adult_28 -model 'cond*group' -mask group_mask_to_standard_2mm_gm_25pc_all_28_R1.nii.gz -jobs 2 -ranEff '~1' -SS_type 3 -num_glt 2 -gltLabel 1 r1-r2 -gltCode 1 'cond : 1*r1 -1*r2' -gltLabel 2 ag_r1-r2 -gltCode 2 'cond : 1*r1 -1*r2 group : 1*ag' -num_glf 1 -glfLabel 1 r1-r2 -glfCode 1 'group : 1*ctr & 1*ag cond : 1*r1 -1*r2' -dataTable Subj cond group InputFile DBD_A00 r1 ag DBD_A00_r1.nii.gz DBD_A00 r2 ag DBD_A00_r2.nii.gz DBD_A03 r1 ag DBD_A03_r1.nii.gz DBD_A03 r2 ag DBD_A03_r2.nii.gz DBD_A05 r1 ag DBD_A05_r1.nii.gz DBD_A05 r2 ag DBD_A05_r2.nii.gz DBD_A06 r1 ag DBD_A06_r1.nii.gz DBD_A06 r2 ag DBD_A06_r2.nii.gz DBD_A07 r1 ag DBD_A07_r1.nii.gz DBD_A07 r2 ag DBD_A07_r2.nii.gz DBD_A08 r1 ag DBD_A08_r1.nii.gz DBD_A08 r2 ag DBD_A08_r2.nii.gz DBD_A10 r1 ag DBD_A10_r1.nii.gz DBD_A10 r2 ag DBD_A10_r2.nii.gz DBD_A11 r1 ag DBD_A11_r1.nii.gz DBD_A11 r2 ag DBD_A11_r2.nii.gz DBD_A15 r1 ag DBD_A15_r1.nii.gz DBD_A15 r2 ag DBD_A15_r2.nii.gz DBD_A20 r1 ag DBD_A20_r1.nii.gz DBD_A20 r2 ag DBD_A20_r2.nii.gz DBD_A21 r1 ag DBD_A21_r1.nii.gz DBD_A21 r2 ag DBD_A21_r2.nii.gz DBD_A22 r1 ag DBD_A22_r1.nii.gz DBD_A22 r2 ag DBD_A22_r2.nii.gz DBD_A23 r1 ag DBD_A23_r1.nii.gz DBD_A23 r2 ag DBD_A23_r2.nii.gz DBD_A24 r1 ag DBD_A24_r1.nii.gz DBD_A24 r2 ag DBD_A24_r2.nii.gz DBD_A25 r1 ag DBD_A25_r1.nii.gz DBD_A25 r2 ag DBD_A25_r2.nii.gz DBD_A26 r1 ag DBD_A26_r1.nii.gz DBD_A26 r2 ag DBD_A26_r2.nii.gz DBD_A27 r1 ag DBD_A27_r1.nii.gz DBD_A27 r2 ag DBD_A27_r2.nii.gz DBD_A28 r1 ag DBD_A28_r1.nii.gz DBD_A28 r2 ag DBD_A28_r2.nii.gz DBD_A01 r1 ctr DBD_A01_r1.nii.gz DBD_A01 r2 ctr DBD_A01_r2.nii.gz DBD_A02 r1 ctr DBD_A02_r1.nii.gz DBD_A02 r2 ctr DBD_A02_r2.nii.gz DBD_A04 r1 ctr DBD_A04_r1.nii.gz DBD_A04 r2 ctr DBD_A04_r2.nii.gz DBD_A09 r1 ctr DBD_A09_r1.nii.gz DBD_A09 r2 ctr DBD_A09_r2.nii.gz DBD_A12 r1 ctr DBD_A12_r1.nii.gz DBD_A12 r2 ctr DBD_A12_r2.nii.gz DBD_A14 r1 ctr DBD_A14_r1.nii.gz DBD_A14 r2 ctr DBD_A14_r2.nii.gz DBD_A16 r1 ctr DBD_A16_r1.nii.gz DBD_A16 r2 ctr DBD_A16_r2.nii.gz DBD_A17 r1 ctr DBD_A17_r1.nii.gz DBD_A17 r2 ctr DBD_A17_r2.nii.gz DBD_A18 r1 ctr DBD_A18_r1.nii.gz DBD_A18 r2 ctr DBD_A18_r2.nii.gz DBD_A19 r1 ctr DBD_A19_r1.nii.gz DBD_A19 r2 ctr DBD_A19_r2.nii.gz
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 *****
28 subjects : DBD_A00 DBD_A01 DBD_A02 DBD_A03 DBD_A04 DBD_A05 DBD_A06 DBD_A07 DBD_A08 DBD_A09 DBD_A10 DBD_A11 DBD_A12 DBD_A14 DBD_A15 DBD_A16 DBD_A17 DBD_A18 DBD_A19 DBD_A20 DBD_A21 DBD_A22 DBD_A23 DBD_A24 DBD_A25 DBD_A26 DBD_A27 DBD_A28
56 response values
2 levels for factor cond : r1 r2
2 levels for factor group : ag ctr
2 post hoc tests

Contingency tables of subject distributions among the categorical variables:


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

r1 r2
DBD_A00 1 1
DBD_A01 1 1
DBD_A02 1 1
DBD_A03 1 1
DBD_A04 1 1
DBD_A05 1 1
DBD_A06 1 1
DBD_A07 1 1
DBD_A08 1 1
DBD_A09 1 1
DBD_A10 1 1
DBD_A11 1 1
DBD_A12 1 1
DBD_A14 1 1
DBD_A15 1 1
DBD_A16 1 1
DBD_A17 1 1
DBD_A18 1 1
DBD_A19 1 1
DBD_A20 1 1
DBD_A21 1 1
DBD_A22 1 1
DBD_A23 1 1
DBD_A24 1 1
DBD_A25 1 1
DBD_A26 1 1
DBD_A27 1 1
DBD_A28 1 1

~~~~~~~~~~~~~~
Subj vs group:

ag ctr
DBD_A00 2 0
DBD_A01 0 2
DBD_A02 0 2
DBD_A03 2 0
DBD_A04 0 2
DBD_A05 2 0
DBD_A06 2 0
DBD_A07 2 0
DBD_A08 2 0
DBD_A09 0 2
DBD_A10 2 0
DBD_A11 2 0
DBD_A12 0 2
DBD_A14 0 2
DBD_A15 2 0
DBD_A16 0 2
DBD_A17 0 2
DBD_A18 0 2
DBD_A19 0 2
DBD_A20 2 0
DBD_A21 2 0
DBD_A22 2 0
DBD_A23 2 0
DBD_A24 2 0
DBD_A25 2 0
DBD_A26 2 0
DBD_A27 2 0
DBD_A28 2 0
***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++

Reading input files now...

** AFNI converts NIFTI_datatype=64 (FLOAT64) in file DBD_A00_r1.nii.gz to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
Reading input files: Done!

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.

[1] "Great, test run passed at voxel (30, 54, 45)!"
[1] "Start to compute 91 slices along Z axis. You can monitor the progress"
[1] "and estimate the total run time as shown below."
[1] "05/30/17 08:18:19.119"
Loading required package: snow
Package snow loaded successfully!

Z slice 1 done: 05/30/17 08:18:21.556
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++ Smallest FDR q [0 (Intercept) F] = 2.12007e-10
++ Smallest FDR q [1 cond F] = 0.0117753
++ Smallest FDR q [2 group F] = 0.00939132
*+ WARNING: Smallest FDR q [3 cond:group F] = 0.466427 ==> few true single voxel detections
++ Smallest FDR q [5 r1-r2 Z] = 2.37392e-07
++ Smallest FDR q [7 ag_r1-r2 Z] = 0.00132016
++ Smallest FDR q [8 r1-r2 Chisq] = 1.07256e-07
[1] "Congratulations! You've got an output DBD_adult_28+tlrc"