I would use a data driven approach like ICA+FIX or ICA-AROMA.  It is not clear that scrubbing is still needed if you use these techniques.

Peace,

Matt.

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of tom parker <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Tuesday, November 3, 2015 at 4:58 AM
To: <[log in to unmask]>
Subject: [FSL] Scrubbing

Dear FSL experts,

I am analyzing resting-state fMRI data for graph theory analyses.

Before extracting the ROI values I would like to apply scrubbing to my data.

At what point in the analysis should I apply scrubbing?

Can I do the following:
Step 1)   motion correction with mcflirt
Step 2)   calculate timepoints with excessive movement with --dvars option
Step 3)   apply scrubbing with fsl_regfit
Step 4)   remove the first timepoints
Step 5)   do slice timing correction
Step 6)   realign
Step 7)   normalize
Step 8)   apply filtering
Step 9)   regress WM and CSF signals
Step 10) extract values of ROIs.

Is this correct? Or should I make the motion correction and scrubbing (Steps 1-3) after Step 8?

Thank you so much!