Hi Harris,

The preprocessing steps sound perfectly fine. You may simply:

a) import your fully-preprocessed MNI-space functional and structural data in the functional and structural tabs, respectively

b) if you have used mcflirt for motion correction enter the resulting .par files in CONN first-level covariates tab as a new covariate named 'realignment'

c) if you have used fsl_motion_outliers for outlier estimation enter the resulting regressor file also as a new first-level covariate now named 'scrubbing' (if you have not run any outlier estimation you may do so from CONN preprocessing tab -select 'functional outlier detection'- on your current data, which will automatically create the 'scrubbing' covariate for you)

After this, you may run any additional preprocessing steps directly from CONN (e.g. spatial smoothing), or you may skip that and proceed directly to the Denoising step. I would probably leave the default Denoising settings (alternatively you may choose to skip aCompCor -e.g. simply by removing the CSF and WhiteMatter ROIs from the 'confounds' list- if you find that somewhat redundant with the Retroicor step you have already run) and from that point on you may proceed normally. 

Hope this helps
Alfonso
Originally posted by Harrison Fisher: