Thanks Alfonso for your reply, this has been extremely helpful. I entered my rp_*.txt files as a first-level covariate named 'motion' and the ART output .mat files named 'outliers' which I specified for each subject in the setup tab for the Covariates 1st-level. All files were located in the same directory. This seems to be working well.

1) The only thing I did differently from my description in my previous post was use the MNI brain template (as well as the grey matter, white matter and csf templates) instead of each individual's wT1 (and segmented GM, WM, and CSF files) – would it be better just to do the latter?

2) I did try specifying 'remove initial scans', for the first four volumes by running this option in the preprocessing step, but received an error. I'm wondering if this was because my rp_*.txt and .mat files had the original number of volumes and if I should have removed the first four before inputting these files at the 1st level. Also, if I do opt to use 'removal of initial scans' from the preprocessing tab, do I need to change the 'duration' time under the conditions tab to account for removal of these four volumes?

3) I went ahead a conducted a second level analysis, to look at between subjects effects in CONN. I specified the contrast 1-1 (1 0; 01) in the between-subject box (to look at differences between patients and controls) and then clicked on the results explorer tab to view the results. My question is: how do I view the results for this contrast in SPM? I tried using the 'spm display', do I simply need to respecify the contrast in the contrast manager window? Is there a way for CONN to implement this without having to respecify a new contrast in SPM?

Thanks so much for your help!!!