Hi Olivier,

Yes, that is exactly the way to skip preprocessing (simply import the already-preprocessed functional and anatomical files, ROI masks, and 1st-level covariates, and then proceed to run the Setup step). The 'import functional data' step is simply importing your functional data to the CONN-specific format used by the rest of steps in CONN, no further preprocessing involved here, and the rest of the steps in Setup will do things like extracting ROI BOLD timeseries, compute principal components of WM/CSF areas, etc., just to have all information necessary to then continue to the Denoising step. 

Hope this helps

Alfonso

Originally posted by Olivier Brown:

Hi there,

 

Our team ran preprocessing steps for our functional data and would like to skip the default pipeline in CONN to proceed with denoising. I imported the anat files, smoothed func files (preprocessing already completed), GM/WM/CSF MNI-space probability masks under ROI, and even the 1st-level covariate data (.txt files for motion parameters [rot & tans x y z], framewise displacement, csf, global signal, wm). 

I made sure not to input anything into the Preprocessing box on the gui. I hit 'Done', as DENOISING is still greyed out, and it begins the process (Steps 1-7; currently at Step 4/7: Importing functional data). Is this still attempting to preprocess the already processed data? Is there a specific way to skip the preprocessing step altogether? I've seen a few posts here regarding this, but cannot determine the exact sequence of steps and info needed to skip the preprocessing and jump to denoising. Any guidance would be appreciated.