Hi Alfonso,
Thank you again for your timely and kind help. It did pull in the 2 sessions of SPM correctly. To follow up this thread, somehow after I use the attached script I reran the set up and denoising steps, it all went through fine and I can check the output without error, but in the first level analysis tab, it'll always give me the error asking me to rerun the setup (see below), then tried reran, but still getting the same error. Is it because the SPMcovariates that automatically imported in might be with different dimensions?
So in my SPM8 1st level design, my regressors of motion might be different across subjects if some of them have no outliers of bad volumes. would this be a problem?

ps, everytime I rerun the setup (by hit done), it takes so long if adding a new 2nd level covariate, is this normal?

I'm attaching the conn.mat file just in case you want to take a look at it to help solve the issue.

Thanks a lot in advance!

ERROR DESCRIPTION:

Error using conn_designmatrix (line 32)
Mismatch info: Please re-run Setup step
Error in conn_process (line 1536)
[X,nill,names]=conn_designmatrix(CONN_x.Analyses(ianalysis).regressors,X1,[]);
Error in conn_process (line 25)
case 'analyses_gui_seed',disp(['CONN: RUNNING ANALYSIS STEP (ROI-to-ROI or seed-to-voxel analyses)']); conn_process([10:12,15],CONN_x.Analysis);
Error in conn (line 3085)
conn_process('analyses_gui_seed',CONN_x.Analysis);
Error in conn_menumanager (line 102)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.14.n
SPM8 + Anatomy ArtRepair Beamforming DEM FieldMap INRIAlign LI MEEGtools PPPI TOM8 aal marsbar wfupickatlas
Matlab v.2012b