Hello,

I have 35 subjects that have undergone 2 different scans in which they have completed a task following 2 different conditions (hence the reason I would like to use 3dLME for the within-subject nature of the study).

For this second level analysis, I would like to first identify "Condition active" voxels that are significantly different from null hypothesis of 0 activity during my contrast [The input file is the activity of contrast 1 - 2] regardless of the condition. I will then extract the average activity from these voxels and compare their activity between the two conditions. It seems like this approach might be possible with 3dttest++ documentation.
"* With 1 set ('-setA'), the mean across input datasets (usually subjects) is tested against 0."

However, I would like to identify this with 3dLME. Should I identify contrast active voxels by combining the clusters from Ex and Rest glt, or maybe the F Condition output? Again, what I am really first trying to identify is all of the clusters of voxels that are "significantly active" for contrast 1-2. And then extract values and compare them across the two conditions (Ex vs. Rest).

Below is the current approach I am trying.

3dLME -prefix AMS_Cond_SimLurevsOldLure_LME_hipp -jobs 6 \
-model 'Cond+Order+Hand+Age' -ranEff '~1' -SS_type 3 \
-num_glt 3 \
-gltLabel 1 'Ex-Rest' -gltCode 1 'Cond : 1*Ex -1*Rest' \
-gltLabel 2 'Ex' -gltCode 2 'Cond : 1*Ex' \
-gltLabel 3 'Rest' -gltCode 3 'Cond : 1*Rest' \
#-mask /Volumes/MRI_BACKUP/test/MTL_MD2mask.nii.gz \
-mask /Volumes/MRI_BACKUP/test/Harvard_bilat_hippocampus_40.nii.gz \
-resid resid_SimLurevsOldLure_lme_hipp.nii.gz \
-qVars "Age" \
-dataTable \
Subj Cond Order Hand Age InputFile \
AMS1001 Ex A R 69 ${fulloutdir}/sub-ams1001/ses-ex/sub-ams1001_ses-ex_REML+tlrc'[81]' \
AMS1002 Ex B R 65 ${fulloutdir}/sub-ams1002/ses-ex/sub-ams1002_ses-ex_REML+tlrc'[81]' \
AMS1003 Ex B L 71 ${fulloutdir}/sub-ams1003/ses-ex/sub-ams1003_ses-ex_REML+tlrc'[81]' \
AMS1004 Ex A R 63 ${fulloutdir}/sub-ams1004/ses-ex/sub-ams1004_ses-ex_REML+tlrc'[81]' \
AMS1005 Ex B R 64 ${fulloutdir}/sub-ams1005/ses-ex/sub-ams1005_ses-ex_REML+tlrc'[81]' \
AMS1006 Ex A R 67 ${fulloutdir}/sub-ams1006/ses-ex/sub-ams1006_ses-ex_REML+tlrc'[81]' \
AMS1007 Ex A R 71 ${fulloutdir}/sub-ams1007/ses-ex/sub-ams1007_ses-ex_REML+tlrc'[81]' \
AMS1008 Ex A R 65 ${fulloutdir}/sub-ams1008/ses-ex/sub-ams1008_ses-ex_REML+tlrc'[81]' \
AMS1009 Ex B L 61 ${fulloutdir}/sub-ams1009/ses-ex/sub-ams1009_ses-ex_REML+tlrc'[81]' \
AMS1010 Ex B R 64 ${fulloutdir}/sub-ams1010/ses-ex/sub-ams1010_ses-ex_REML+tlrc'[81]' \
AMS1011 Ex B R 65 ${fulloutdir}/sub-ams1011/ses-ex/sub-ams1011_ses-ex_REML+tlrc'[81]' \
AMS1012 Ex A R 64 ${fulloutdir}/sub-ams1012/ses-ex/sub-ams1012_ses-ex_REML+tlrc'[81]' \
AMS1013 Ex B R 70 ${fulloutdir}/sub-ams1013/ses-ex/sub-ams1013_ses-ex_REML+tlrc'[81]' \
AMS1014 Ex A R 75 ${fulloutdir}/sub-ams1014/ses-ex/sub-ams1014_ses-ex_REML+tlrc'[81]' \
AMS1015 Ex A R 69 ${fulloutdir}/sub-ams1015/ses-ex/sub-ams1015_ses-ex_REML+tlrc'[81]' \
AMS1016 Ex B R 66 ${fulloutdir}/sub-ams1016/ses-ex/sub-ams1016_ses-ex_REML+tlrc'[81]' \
AMS1017 Ex B R 60 ${fulloutdir}/sub-ams1017/ses-ex/sub-ams1017_ses-ex_REML+tlrc'[81]' \
#AMS1018 Ex A R 62 ${fulloutdir}/sub-ams1018/ses-ex/sub-ams1018_ses-ex_REML+tlrc'[81]' \
AMS1019 Ex B R 70 ${fulloutdir}/sub-ams1019/ses-ex/sub-ams1019_ses-ex_REML+tlrc'[81]' \
#AMS1020 Ex A R 76 ${fulloutdir}/sub-ams1020/ses-ex/sub-ams1020_ses-ex_REML+tlrc'[81]' \
AMS1021 Ex A R 69 ${fulloutdir}/sub-ams1021/ses-ex/sub-ams1021_ses-ex_REML+tlrc'[81]' \
AMS1022 Ex A R 72 ${fulloutdir}/sub-ams1022/ses-ex/sub-ams1022_ses-ex_REML+tlrc'[81]' \
AMS1023 Ex B R 66 ${fulloutdir}/sub-ams1023/ses-ex/sub-ams1023_ses-ex_REML+tlrc'[81]' \
AMS1024 Ex B L 73 ${fulloutdir}/sub-ams1024/ses-ex/sub-ams1024_ses-ex_REML+tlrc'[81]' \
#AMS1025 Ex B R 60 ${fulloutdir}/sub-ams1025/ses-ex/sub-ams1025_ses-ex_REML+tlrc'[81]' \
AMS1026 Ex B R 76 ${fulloutdir}/sub-ams1026/ses-ex/sub-ams1026_ses-ex_REML+tlrc'[81]' \
AMS1027 Ex B R 62 ${fulloutdir}/sub-ams1027/ses-ex/sub-ams1027_ses-ex_REML+tlrc'[81]' \
AMS1028 Ex A R 69 ${fulloutdir}/sub-ams1028/ses-ex/sub-ams1028_ses-ex_REML+tlrc'[81]' \
AMS1029 Ex A R 74 ${fulloutdir}/sub-ams1029/ses-ex/sub-ams1029_ses-ex_REML+tlrc'[81]' \
AMS1030 Ex A R 74 ${fulloutdir}/sub-ams1030/ses-ex/sub-ams1030_ses-ex_REML+tlrc'[81]' \
#AMS1031 Ex B L 70 ${fulloutdir}/sub-ams1031/ses-ex/sub-ams1031_ses-ex_REML+tlrc'[81]' \
AMS1032 Ex B R 61 ${fulloutdir}/sub-ams1032/ses-ex/sub-ams1032_ses-ex_REML+tlrc'[81]' \
AMS1033 Ex A R 65 ${fulloutdir}/sub-ams1033/ses-ex/sub-ams1033_ses-ex_REML+tlrc'[81]' \
#AMS1034 Ex B L 60 ${fulloutdir}/sub-ams1034/ses-ex/sub-ams1034_ses-ex_REML+tlrc'[81]' \
AMS1035 Ex A R 68 ${fulloutdir}/sub-ams1035/ses-ex/sub-ams1035_ses-ex_REML+tlrc'[81]' \
AMS1037 Ex B R 70 ${fulloutdir}/sub-ams1037/ses-ex/sub-ams1037_ses-ex_REML+tlrc'[81]' \
AMS1038 Ex B R 65 ${fulloutdir}/sub-ams1038/ses-ex/sub-ams1038_ses-ex_REML+tlrc'[81]' \
AMS1039 Ex B R 64 ${fulloutdir}/sub-ams1039/ses-ex/sub-ams1039_ses-ex_REML+tlrc'[81]' \
AMS1040 Ex B R 62 ${fulloutdir}/sub-ams1040/ses-ex/sub-ams1040_ses-ex_REML+tlrc'[81]' \
AMS1041 Ex A R 67 ${fulloutdir}/sub-ams1041/ses-ex/sub-ams1041_ses-ex_REML+tlrc'[81]' \
AMS1001 Rest A R 69 ${fulloutdir}/sub-ams1001/ses-rest/sub-ams1001_ses-rest_REML+tlrc'[81]' \
AMS1002 Rest B R 65 ${fulloutdir}/sub-ams1002/ses-rest/sub-ams1002_ses-rest_REML+tlrc'[81]' \
AMS1003 Rest B L 71 ${fulloutdir}/sub-ams1003/ses-rest/sub-ams1003_ses-rest_REML+tlrc'[81]' \
AMS1004 Rest A R 63 ${fulloutdir}/sub-ams1004/ses-rest/sub-ams1004_ses-rest_REML+tlrc'[81]' \
AMS1005 Rest B R 64 ${fulloutdir}/sub-ams1005/ses-rest/sub-ams1005_ses-rest_REML+tlrc'[81]' \
AMS1006 Rest A R 67 ${fulloutdir}/sub-ams1006/ses-rest/sub-ams1006_ses-rest_REML+tlrc'[81]' \
AMS1007 Rest A R 71 ${fulloutdir}/sub-ams1007/ses-rest/sub-ams1007_ses-rest_REML+tlrc'[81]' \
AMS1008 Rest A R 65 ${fulloutdir}/sub-ams1008/ses-rest/sub-ams1008_ses-rest_REML+tlrc'[81]' \
AMS1009 Rest B L 61 ${fulloutdir}/sub-ams1009/ses-rest/sub-ams1009_ses-rest_REML+tlrc'[81]' \
AMS1010 Rest B R 64 ${fulloutdir}/sub-ams1010/ses-rest/sub-ams1010_ses-rest_REML+tlrc'[81]' \
AMS1011 Rest B R 65 ${fulloutdir}/sub-ams1011/ses-rest/sub-ams1011_ses-rest_REML+tlrc'[81]' \
AMS1012 Rest A R 64 ${fulloutdir}/sub-ams1012/ses-rest/sub-ams1012_ses-rest_REML+tlrc'[81]' \
AMS1013 Rest B R 70 ${fulloutdir}/sub-ams1013/ses-rest/sub-ams1013_ses-rest_REML+tlrc'[81]' \
AMS1014 Rest A R 75 ${fulloutdir}/sub-ams1014/ses-rest/sub-ams1014_ses-rest_REML+tlrc'[81]' \
AMS1015 Rest A R 69 ${fulloutdir}/sub-ams1015/ses-rest/sub-ams1015_ses-rest_REML+tlrc'[81]' \
AMS1016 Rest B R 66 ${fulloutdir}/sub-ams1016/ses-rest/sub-ams1016_ses-rest_REML+tlrc'[81]' \
AMS1017 Rest B R 60 ${fulloutdir}/sub-ams1017/ses-rest/sub-ams1017_ses-rest_REML+tlrc'[81]' \
#AMS1018 Rest A R 62 ${fulloutdir}/sub-ams1018/ses-rest/sub-ams1018_ses-rest_REML+tlrc'[81]' \
AMS1019 Rest B R 70 ${fulloutdir}/sub-ams1019/ses-rest/sub-ams1019_ses-rest_REML+tlrc'[81]' \
#AMS1020 Rest A R 76 ${fulloutdir}/sub-ams1020/ses-rest/sub-ams1020_ses-rest_REML+tlrc'[81]' \
AMS1021 Rest A R 69 ${fulloutdir}/sub-ams1021/ses-rest/sub-ams1021_ses-rest_REML+tlrc'[81]' \
AMS1022 Rest A R 72 ${fulloutdir}/sub-ams1022/ses-rest/sub-ams1022_ses-rest_REML+tlrc'[81]' \
AMS1023 Rest B R 66 ${fulloutdir}/sub-ams1023/ses-rest/sub-ams1023_ses-rest_REML+tlrc'[81]' \
AMS1024 Rest B L 73 ${fulloutdir}/sub-ams1024/ses-rest/sub-ams1024_ses-rest_REML+tlrc'[81]' \
#AMS1025 Rest B R 60 ${fulloutdir}/sub-ams1025/ses-rest/sub-ams1025_ses-rest_REML+tlrc'[81]' \
AMS1026 Rest B R 76 ${fulloutdir}/sub-ams1026/ses-rest/sub-ams1026_ses-rest_REML+tlrc'[81]' \
AMS1027 Rest B R 76 ${fulloutdir}/sub-ams1027/ses-rest/sub-ams1027_ses-rest_REML+tlrc'[81]' \
AMS1028 Rest A R 69 ${fulloutdir}/sub-ams1028/ses-rest/sub-ams1028_ses-rest_REML+tlrc'[81]' \
AMS1029 Rest A R 74 ${fulloutdir}/sub-ams1029/ses-rest/sub-ams1029_ses-rest_REML+tlrc'[81]' \
AMS1030 Rest A R 60 ${fulloutdir}/sub-ams1030/ses-rest/sub-ams1030_ses-rest_REML+tlrc'[81]' \
#AMS1031 Rest B L 70 ${fulloutdir}/sub-ams1031/ses-rest/sub-ams1031_ses-rest_REML+tlrc'[81]' \
AMS1032 Rest B R 61 ${fulloutdir}/sub-ams1032/ses-rest/sub-ams1032_ses-rest_REML+tlrc'[81]' \
AMS1033 Rest A R 65 ${fulloutdir}/sub-ams1033/ses-rest/sub-ams1033_ses-rest_REML+tlrc'[81]' \
#AMS1034 Rest B L 60 ${fulloutdir}/sub-ams1034/ses-rest/sub-ams1034_ses-rest_REML+tlrc'[81]' \
AMS1035 Rest A R 68 ${fulloutdir}/sub-ams1035/ses-rest/sub-ams1035_ses-rest_REML+tlrc'[81]' \
AMS1037 Rest B R 70 ${fulloutdir}/sub-ams1037/ses-rest/sub-ams1037_ses-rest_REML+tlrc'[81]' \
AMS1038 Rest B R 65 ${fulloutdir}/sub-ams1038/ses-rest/sub-ams1038_ses-rest_REML+tlrc'[81]' \
AMS1039 Rest B R 64 ${fulloutdir}/sub-ams1039/ses-rest/sub-ams1039_ses-rest_REML+tlrc'[81]' \
AMS1040 Rest B R 62 ${fulloutdir}/sub-ams1040/ses-rest/sub-ams1040_ses-rest_REML+tlrc'[81]' \
AMS1041 Rest A R 67 ${fulloutdir}/sub-ams1041/ses-rest/sub-ams1041_ses-rest_REML+tlrc'[81]'
'

Any help modeling this with 3dLME (if possible) would be greatly appreciated!



Edited 1 time(s). Last edit at 09/22/2022 09:00PM by 2Daniel4.