First and foremost, please let me thank you for all the help.  I firmly believe the success of this wonderful toolbox is largely due to the responsiveness of the forum.

I had a question about the denoising process for resting fMRI comparisons in a 2 x 2, repeated measures model (Time x Group).  Taking your recommendations from earlier about how to set up a repeated measures model, I performed the following with associated settings:


ROIs:
Grey Matter
White Matter - Regress out covariates
CSF - Regress out covariates
rsREL - Multiple ROIs
AAL - Multiple ROIs

Conditions:
Rest_base
Rest_6wk

Subjects (n = 24)

Sessions:
Session 1 = Baseline
Session 2 = 6wk

First-Level Covariates:
None

Second-Level Covariates:
AllSubjects
Controls = 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0
Patients = 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1

Denoising Options:
Confounds:
White Matter
CSF
Effect of Rest_base
Effect of Rest_6wk

Band-pass filter (0.008 0.09; after regression)
Linear detrending
Despiking after regression

Second-level Analysis:
Subject effects:
All Subjects
Controls
Patients

Between-subjects contrast: 0 1 -1

Conditions:
Rest_base
Rest_6wk

Between-conditions contrast: -1 1

Sources:
AAL_Hipp(L)
AAL_Hipp(R)

Between-sources contrast: 0 1; 1 0

I'm hoping the above will show where control group ALL ROI hippocampal connectivity is greater than patients at 6wks, but I had a question about the denoising process including the "Effect of Rest_base" and "Effect of Rest_6wk."  Is this correct?

Also, any other recommendations to the above settings?

Thanks again and warm regards.  Happy holidays to all!

Jeff