Hmm thanks for checking! I'll go through the processing steps in case I did anything wrong beforehand.

As I stated, there are 2 groups (MDD and HC). There are two fMRI sessions per subject. In each session, there are 2 runs of the task.

Here are the processing steps I do per subject per session:

1. Run fmriprep
2. Preprocess: smooth, remove 5 first TRs, zscore each voxel over time
3. Run AFNI 3dDeconvolve across both runs of the task using the command:
   cmd = ("3dDeconvolve -polort A "
   "-input "
   "{0}/{1}/{2}/{1}_{2}_task-faces_rec-uncorrected_run-01_bold_space-MNI152NLin2009cAsym_preproc.nii.gz "
   "{0}/{1}/{2}/{1}_{2}_task-faces_rec-uncorrected_run-02_bold_space-MNI152NLin2009cAsym_preproc.nii.gz "
   "-mask {8} "
   "-num_glt 2 "
   "-local_times -num_stimts 4 "
   " {3} {4} {5} {6} "
   "-gltsym 'SYM: +happy -neutral' -glt_label 1 'happyvsneut' "
   "-gltsym 'SYM: +fearful -neutral' -glt_label 2 'fearvsneut' "
   "-ortvec {7} "
   "-fout -tout -x1D {9}/{1}/{2}/{1}_{2}_task-faces_glm.X.xmat.1D " # this is the actual design matrix
   "-xjpeg {9}/{1}/{2}/{1}_{2}_task-faces_glm.X.jpg " # this is the design matrix
   "-fitts {9}/{1}/{2}/{1}_{2}_task-faces_glm.fitts " # model prediction - betas * signal
   "-errts {9}/{1}/{2}/{1}_{2}_task-faces.errts " # residuals
   "-bucket {9}/{1}/{2}/{1}_{2}_task-faces_glm.stats".format(run_path,
   bids_id, ses_id, neutral_reg, object_reg, happy_reg, fearful_reg,full_save_path,whole_brain_mask,analyses_out ))

And then I have the following steps for group level analysis:

1. Subtract session 3 - session 1 betas for each subject using 3dcalc
   cmd = ("3dcalc -a {0} ".format(subject_stats_2) +
   "-b {0} ".format(subject_stats_1) +
   "-expr 'a-b' -prefix {0}".format(output))
2. Calculate covariates from Framewise displacement (I think I did this right, but just to be sure, the first column lists the subject name that's used later in 3dttest++. The order of the subjects listed as rows in the covariate file is *not* the order of the subjects listed in 3dttest++.)
3. Run 3dttest++ on the differences between sessions across groups with the command printed above:
   command = ("3dttest++ -setA {0} ".format(MDD_subj_str) +
   "-setB {0} ".format(HC_subj_str) +
   "-prefix {0}/ses-03_minus_ses-01/ses-03_minus_ses-01_stats_{1}_ACC_dlPFC_mask.ttest.nii.gz ".format(second_level,BRIK_KEY[BRIK]) +
   "-AminusB "
   "-mask {0} ".format(dlPFC_mask) +
   "-covariates {0} ".format(covar_file) +
   "-prefix_clustsim ses-03_minus_ses-01_stats_{0}_ACC_dlPFC_mask ".format(BRIK_KEY[BRIK]) +
   "-ETAC -ETAC_blur 0 4 6 8 " +
   "-ETAC_opt NN=2:sid=1:hpow=0:name=test1:pthr=0.01/0.001/10:fpr=5"
   )

I checked the results from running 3dttest++ and ETAC on individual sessions, instead of subtracted data across sessions. I still see inconsistency between 3dttest results and ETAC one-sided masks. So I'm not sure what I'm doing wrong here :/

Thanks for your help!