Dear AFNI folks,
I’m trying to use 3dLME to get an estimate of voxelwise ICC. The design is as follows: a group of subjects were scanned about a week apart. I entered the contrast estimates for our task contrast of interest into 3dLME using the following command:
3dLME -prefix LME_Embarc_HC_ICC_iI-cI_80Acc4mmRMS_WB
-model “1”
-ranEff ‘Subj+Time’
-ICC
-dataTable
Subj Time InputFile
CU0009 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/CU0009CUMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
CU0009 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/CU0009CUMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
CU0013 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/CU0013CUMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
CU0013 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/CU0013CUMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
CU0017 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/CU0017CUMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
CU0017 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/CU0017CUMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
CU0018 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/CU0018CUMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
CU0018 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/CU0018CUMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
CU0020 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/CU0020CUMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
CU0020 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/CU0020CUMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
CU0023 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/CU0023CUMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
CU0023 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/CU0023CUMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
CU0028 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/CU0028CUMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
CU0028 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/CU0028CUMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
MG0006 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/MG0006MGMR1R2_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
MG0006 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/MG0006MGMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
MG0007 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/MG0007MGMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
MG0007 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/MG0007MGMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
MG0008 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/MG0008MGMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
MG0008 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/MG0008MGMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
MG0020 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/MG0020MGMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
MG0020 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/MG0020MGMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
MG0025 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/MG0025MGMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
MG0025 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/MG0025MGMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
MG0026 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/MG0026MGMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
MG0026 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/MG0026MGMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
MG0028 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/MG0028MGMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
MG0028 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/MG0028MGMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
MG0030 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/MG0030MGMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
MG0030 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/MG0030MGMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
MG0040 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/MG0040MGMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
MG0040 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/MG0040MGMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
MG0081 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/MG0081MGMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
MG0081 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/MG0081MGMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
TX0016 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/TX0016TXMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
TX0016 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/TX0016TXMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
TX0019 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/TX0019TXMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
TX0019 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/TX0019TXMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
TX0022 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/TX0022TXMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
TX0022 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/TX0022TXMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
TX0027 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/TX0027TXMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
TX0027 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/TX0027TXMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
TX0029 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/TX0029TXMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
TX0029 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/TX0029TXMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
TX0033 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/TX0033TXMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
TX0033 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/TX0033TXMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
TX0037 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/TX0037TXMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
TX0037 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/TX0037TXMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
TX0038 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/TX0038TXMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
TX0038 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/TX0038TXMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
TX0040 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/TX0040TXMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
TX0040 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/TX0040TXMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
TX0041 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/TX0041TXMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
TX0041 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/TX0041TXMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
UM0012 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/UM0012UMMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
UM0012 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/UM0012UMMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
UM0017 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/UM0017UMMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
UM0017 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/UM0017UMMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
UM0023 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/UM0023UMMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
UM0023 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/UM0023UMMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
UM0024 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/UM0024UMMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
UM0024 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/UM0024UMMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
UM0029 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/UM0029UMMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
UM0029 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/UM0029UMMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
UM0031 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/UM0031UMMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
UM0031 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/UM0031UMMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
UM0032 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/UM0032UMMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
UM0032 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/UM0032UMMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
UM0035 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/UM0035UMMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
UM0035 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/UM0035UMMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
UM0040 PreTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session1/all_con_0005_mni_fonz/emoconflict_with_motion/UM0040UMMR1R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
UM0040 PostTx /Volumes/Smurf-Village/Imaging/embarc/full_data/emoconflict/session2/all_con_0005_mni_fonz/emoconflict_with_motion/UM0040UMMR2R1_emoconflict_emoconflict_with_motion_con_0005_mni.nii.gz
The output from 3dLME, however, has 0 values for the ICC across most of the brain. See attached screenshot for reference.
I’m wondering whether I did something incorrectly with the command, or if the ICC is just so poor for most of the brain that the program is rounding the output to 0 across most voxels?
Any help would be much appreciated! Thanks for your time.
Best,
Greg
