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You can do the same thing as scrubbing by making regressors of the form 0000100000 for a toy example with 10 frames where you want to remove all variance from frame 5. Peace, Matt. From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of lukebaxter <[log in to unmask]> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Date: Tuesday, April 4, 2017 at 7:19 PM To: <[log in to unmask]> Subject: Re: [FSL] How to delete volumes (scrubbing) using fsl? Hi Matt, Thank you for your reply. The data has already been cleaned a la HCP. It is neonatal data, so in fact, it has been analysed with the developing HCP (dHCP) pipeline, which includes ICA-FIX de-noising. Since the data is from neonates, it has an unusually high level of motion artefacts, even after going through the dHCP pipeline. I would like to compare the effects of 'dHCP-style pre-processing' alone to 'dHCP-style pre-processing + scrubbing'. It is simply exploratory, and scrubbing may not be included in the end, but I would like to experiment with it all the same. I'm sure there is a simpler way to implement scrubbing, than the ways I've already outlined. If a simpler method for scrubbing is known, please let me know. All the best, Luke. > On 4 Apr 2017, at 21:09, Matt Glasser <[log in to unmask]> wrote: > > If you are doing an ICA analysis, I recommend cleaning your data with ICA+FIX > if it is HCP-Style (high spatial/temporal resolution) or ICA-AROMA if it isnıt > rather than scrubbing. > > Peace, > > Matt. > > From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of > lukebaxter <[log in to unmask]> > Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> > Date: Tuesday, April 4, 2017 at 2:15 PM > To: <[log in to unmask]> > Subject: Re: [FSL] How to delete volumes (scrubbing) using fsl? > > Hi Eugene and Matthew, > > Thank you for your helpful feedback. > > Matthew, I wonıt be using my resting state data in a feat analysis, so I canıt > use that approach unfortunately. I will be inputting my denoised data into an > ICA analysis. > > Eugene, I have already denoised the data using melodic and fsl_regfilt. I have > then run fsl_motion_outliers on this fully denoised data to find motion > artefacts that I canıt seem to remove with the other pre-processing steps. The > remaining motion (measured using dvars) is indeed greatly reduced in the fully > denoised data compared to the pre-denoised data, but there are still some > relatively large spikes remaining. I was hoping to remove these very few > troublesome volumes by scrubbing. > > I hope thatıs clear. Let me know if not. > > Luke. > > >> On 4 Apr 2017, at 17:10, Eugene Duff <[log in to unmask]> wrote: >> >> Hi - >> >> On 4 April 2017 at 17:06, Matthew Webster <[log in to unmask]> >> wrote: >>> 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. >>> >> >> If you're not doing a FEAT analysis (e.g. ICA), it may not be useful to >> remove this volumes. ICA should be able to separate these artefacts itself, >> and these components may also pick up smaller artefacts than are defined by >> the scrubbing. >> >> >> Eugene >> >> >> >>> 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. >> >