Hi, I’m running a traditional (not gPPI) PPI analysis using 3dDeconvolve. I want to do this across four runs per subject, so I am trying to concatenate all runs in time by inputting them all into 3dDeconvolve at once, but the design matrix i get out is not what i expected. Could someone tell me what I’m doing wrong?
my 3dDeconvolve script is as follows for one subject and their four runs:
3ddeconvolve -polort A -jobs 1 -mask preproc/sub-002/func/sub-002_task-sexemo_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz -input preproc/sub-002/func/sub-002_task-sexemo_run-01_smoothed.nii.gz preproc/sub-002/func/sub-002_task-sexemo_run-02_smoothed.nii.gz preproc/sub-002/func/sub-002_task-sexemo_run-03_smoothed.nii.gz preproc/sub-002/func/sub-002_task-sexemo_run-04_smoothed.nii.gz -bucket analysis/func_conn/average/nSynth_face_rFG/sub-002_bucket.nii.gz -fout -tout -rout -xjpegpreproc/sub-002/func/sub-002_designmatrix.jpg -nfirst 0 -num_stimts 13 -stim_times 1 preproc/events_subliminal.1D 'GAM' -stim_label 1 subliminal -stim_times 2 preproc/events_supraliminal.1D 'GAM' -stim_label 2 supraliminal -stim_file 3 analysis/GLM_1Ds/sub-002_confounds_csf.1D -stim_base 3 -stim_label 3 csf -stim_file 4 analysis/GLM_1Ds/sub-002_confounds_global_signal.1D -stim_base 4 -stim_label 4 global_signal -stim_file 5 analysis/GLM_1Ds/sub-002_confounds_rot_x.1D -stim_base 5 -stim_label 5 rot_x -stim_file 6 analysis/GLM_1Ds/sub-002_confounds_rot_y.1D -stim_base 6 -stim_label 6 rot_y -stim_file 7 analysis/GLM_1Ds/sub-002_confounds_rot_z.1D -stim_base 7 -stim_label 7 rot_z -stim_file 8 analysis/GLM_1Ds/sub-002_confounds_trans_x.1D -stim_base 8 -stim_label 8 trans_x -stim_file 9 analysis/GLM_1Ds/sub-002_confounds_trans_y.1D -stim_base 9 -stim_label 9 trans_y -stim_file 10 analysis/GLM_1Ds/sub-002_confounds_trans_z.1D -stim_base 10 -stim_label 10 trans_z -stim_file 11 analysis/GLM_1Ds/sub-002_confounds_white_matter.1D -stim_base 11 -stim_label 11 white_matter -stim_file 12 preproc/sub-002/func/sub-002_seed_ts_all_nSynth_face_rFG.1D -stim_label 12 Seed_ts -stim_file 13 preproc/sub-002/func/sub-002_inter_ts_nSynth_face_rFG.1D -stim_label 13 Inter_ts
Which to my mind should output a Design matrix of 13868 (868 = n TRs, since 217 per run and 2174 =868) and 13 columns, since we have 13 stim files (4 regressors of interest including the PPI regressors and 9 confound variables). However, the design matrix i get out (attached) has 29 columns, some of which I have no idea about. Moreover, the pattern for what I think are the regressors of interest seem to be repeating across runs, rather than being different for each run. I am inputting event timing 1D files that are 868 length, i.e. the length of all 4 runs combined. Perhaps its reading only the first 217 for each run? How do I specify different event files for each run in this case, whilst still concatenating runs in time within 3dDeconvolve (i.e. not having to do separate 3dDeconvolve scripts for each run).
I’ve attached the design matrix for this subject for your reference, the last 9 columns appear to be the confound regressors, but what are the preceding 20? Hace I done this correctly?