Dear AFNI experts,

I am trying to understand the difference between 3dLME vs. 3dMVM GLT contrasts.

In brief, I have a model with all within-subjects variables of interest: 3 time (TRs), 2 scan sessions, and 2 attention conditions. I also have some nuisance factors that I am not interested (e.g., participants’ scan sequence orders, body weights, scan time onsets; all centered at 0 across subjects). Because of these nuisance factors, I have decided to run 3dLME framework. I am defining many different contrasts using GLT set up (attached below). Without the nuisance factors, I also have run the very similar GLT’s under 3dMVM.

The big discrepancy I see is that the effect seems to be very big under 3dLME compared to 3dMVM. For instance, for the 1st GLT, I see a very large region showing a significant contrast under 3dLME, but greatly reduced # of voxels under 3dMVM at the same uncorrected thresholds. It almost feels like 3dLME inflates this contrast.

Could you give me a pointer whether my model specification is correct for the conditions that I have? In essence, I am not so interested in time (TR) factor, but rather interested in 2 scan session (DO and PL) and attType (such as GLT # 1, 2, 21, 25, 26, 27).
Would it be more appropriate to run it under 3dMVM?

Thank you very much for your help!
Michelle.

3dLME \
-prefix ../ANOVA_results/3dLME_VvsN_CueRetProbeTENT-2-4TRs_x_attType_x_scanType-allCOVs_final.nii \
-jobs 1 \
-model 'scanType*attType*timeTR+sequence+weight+scanTime' \
-qVars ‘sequence,weight,scanTime' \
-qVarCenters '0,0,0' \
-ranEff '~1' \
-num_glt 27 \
-gltLabel 1 ‘DO-PL’ -gltCode 1 'scanType : 1*D -1*P' \
-gltLabel 2 'Valid-Neutral' -gltCode 2 'attType : 1*V -1*N' \
-gltLabel 3 'Valid-Neutral_4s' -gltCode 3 'attType : 1*V -1*N timeTR : 1*t2' \
-gltLabel 4 'Valid-Neutral_6s' -gltCode 4 'attType : 1*V -1*N timeTR : 1*t3' \
-gltLabel 5 'Valid-Neutral_8s' -gltCode 5 'attType : 1*V -1*N timeTR : 1*t4' \
-gltLabel 6 'attType_x_scanType_4s' -gltCode 6 'attType : 1*V -1*N scanType : 1*D -1*P timeTR : 1*t2' \
-gltLabel 7 'attType_x_scanType_6s' -gltCode 7 'attType : 1*V -1*N scanType : 1*D -1*P timeTR : 1*t3' \
-gltLabel 8 'attType_x_scanType_8s' -gltCode 8 'attType : 1*V -1*N scanType : 1*D -1*P timeTR : 1*t4' \
-gltLabel 9 'DO-PL_Neutral_4s' -gltCode 9 'attType : 1*N scanType : 1*D -1*P timeTR : 1*t2' \
-gltLabel 10 'DO-PL_Neutral_6s' -gltCode 10 'attType : 1*N scanType : 1*D -1*P timeTR : 1*t3' \
-gltLabel 11 'DO-PL_Neutral_8s' -gltCode 11 'attType : 1*N scanType : 1*D -1*P timeTR : 1*t4' \
-gltLabel 12 'DO-PL_Valid_4s' -gltCode 12 'attType : 1*V scanType : 1*D -1*P timeTR : 1*t2' \
-gltLabel 13 'DO-PL_Valid_6s' -gltCode 13 'attType : 1*V scanType : 1*D -1*P timeTR : 1*t3' \
-gltLabel 14 'DO-PL_Valid_8s' -gltCode 14 'attType : 1*V scanType : 1*D -1*P timeTR : 1*t4' \
-gltLabel 15 'DO-PL_at_4s' -gltCode 15 'scanType : 1*D -1*P timeTR : 1*t2' \
-gltLabel 16 'DO-PL_at_6s' -gltCode 16 'scanType : 1*D -1*P timeTR : 1*t3' \
-gltLabel 17 'DO-PL_at_8s' -gltCode 17 'scanType : 1*D -1*P timeTR : 1*t4' \
-gltLabel 18 'DO_Valid-Neutral_4s' -gltCode 18 'scanType : 1*D attType : 1*V -1*N timeTR : 1*t2' \
-gltLabel 19 'DO_Valid-Neutral_6s' -gltCode 19 'scanType : 1*D attType : 1*V -1*N timeTR : 1*t3' \
-gltLabel 20 'DO_Valid-Neutral_8s' -gltCode 20 'scanType : 1*D attType : 1*V -1*N timeTR : 1*t4' \
-gltLabel 21 'DO_Valid-Neutral_allTRs' -gltCode 21 'scanType : 1*D attType : 1*V -1*N' \
-gltLabel 22 'PL_Valid-Neutral_4s' -gltCode 22 'scanType : 1*P attType : 1*V -1*N timeTR : 1*t2' \
-gltLabel 23 'PL_Valid-Neutral_6s' -gltCode 23 'scanType : 1*P attType : 1*V -1*N timeTR : 1*t3' \
-gltLabel 24 'PL_Valid-Neutral_8s' -gltCode 24 'scanType : 1*P attType : 1*V -1*N timeTR : 1*t4' \
-gltLabel 25 'PL_Valid-Neutral_allTRs' -gltCode 25 'scanType : 1*P attType : 1*V -1*N' \
-gltLabel 26 'DO-PL_Neutral_allTRs' -gltCode 26 'attType : 1*N scanType : 1*D -1*P' \
-gltLabel 27 'DO-PL_Valid_allTRs' -gltCode 27 'attType : 1*V scanType : 1*D -1*P' \
-mask /Users/sungjoo/DATA/RETROCUE_fMRI/GroupMask/mask_group_N=22_fromNative+tlrc. \
-resid ../ANOVA_results/resid_3dLME_VvsN_CueRetProbeTENT-2-4TRs_x_attType_x_scanType-allCOVs_final_corStr.nii \
-dataTable \
Subj sequence weight scanTime scanType attType timeTR InputFile \
Ss_210 1 -0.63657 -1.36364 D V t2 ../../Ss_210/session2/allRuns_tlrc_e2a_censor_noss_smooth_native/stats_test_cueContrast_allfields_CueRetProbeTENT_tlrc.Ss_210+tlrc'[79]' \
Ss_212 -1 0.95703 -1.36364 D V t2 ../../Ss_212/session1/allRuns_tlrc_e2a_censor_noss_smooth_native/stats_test_cueContrast_allfields_CueRetProbeTENT_tlrc.Ss_212+tlrc'[79]' \
…



Edited 1 time(s). Last edit at 06/02/2017 02:35PM by sjmich.