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Hello, If you will be using your resting-state data in ( e.g. ) a FEAT analysis, then the confound matrix just needs to be added as a confound in the Stats tab in the FEAT GUI to account for the outliers. Kind Regards Matthew > On 4 Apr 2017, at 16:46, Luke Baxter <[log in to unmask]> wrote: > > Hi, > > I would like to take the output of fsl_motion_outliers and delete those volumes from my resting state data that have been deemed outliers. My resting state scan has 500 volumes, and there are on average 25 outliers per scan to be scrubbed. > > Using fsl_split, manually deleting volumes, then using fsl_merge is quite a long and tedious manual approach. Similarly, using fslroi to isolate chunks of the scan between outliers is not ideal, because the outliers aren't clumping together much, so there would be about 20 chunks. Again, very tedious. > > Is there a way of taking the output of fsl_motion_outliers, and perhaps multiplying this by my resting state nifti, to delete the outlier volumes? Has anyone discovered a simple approach, or is there one already available in fsl? > > Any info would be greatly appreciated. > > Cheers, > Luke.