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FD of motion correction after having already run motion correction is not going to be a valid metric. Matt. From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of "[log in to unmask]<mailto:[log in to unmask]>" <[log in to unmask]<mailto:[log in to unmask]>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> Date: Tuesday, October 2, 2018 at 10:44 AM To: "[log in to unmask]<mailto:[log in to unmask]>" <[log in to unmask]<mailto:[log in to unmask]>> Subject: Re: [FSL] FD before and after FIX Thanks for your response! Maybe I wasn't clear before or maybe I am getting it wrong. I run fsl_motion_outliers with the option -nomoco just to get the FD before and after denoising to see how different they are. But I do run motion correction as part of single-session ICA. And yes, I do expected to see a big difference because I have already realigned the data. My purpose is to check the parameters again and see whether FD after denoising still meets the exclusion criteria or not. Please let me know if that approach is wrong? Thanks, Sara ________________________________ From: FSL - FMRIB's Software Library [[log in to unmask]<mailto:[log in to unmask]>] on behalf of Glasser, Matthew [[log in to unmask]<mailto:[log in to unmask]>] Sent: Tuesday, October 02, 2018 4:05 AM To: [log in to unmask]<mailto:[log in to unmask]> Subject: Re: [FSL] FD before and after FIX This doesn’t make a whole lot of sense to me. If you’ve already spatially realigned the data, wouldn’t you expect that further spatial realignment wouldn’t make much difference (and thus a recomputed FD would be low)? In any case, FIX should remove the temporal effects of motion from the data, given sufficient data quality, though not of global physiological noise. Some of these issues are discussed here: https://www.sciencedirect.com/science/article/pii/S1053811918303963 Matt. From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of Steve Smith <[log in to unmask]<mailto:[log in to unmask]>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> Date: Tuesday, October 2, 2018 at 1:15 AM To: "[log in to unmask]<mailto:[log in to unmask]>" <[log in to unmask]<mailto:[log in to unmask]>> Subject: Re: [FSL] FD before and after FIX Hi - I'm a bit confused here because we don't run motion correction a second time after FIX. I'm not saying it's a bad thing - we've just never tested that out and I don't have a very clear feeling about what I'd expect. Anyway - yes FIX is aiming to remove many sources of artefact including those related to head motion, so yes if it's working well it should be able to salvage subjects' data which is otherwise unusable (or requires alternate motion fixing methods). Cheers. On 1 Oct 2018, at 18:42, [log in to unmask]<mailto:[log in to unmask]> <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi FSL team, I am working with resting state data obtained from children with neurodevelopmental disorders like ADHD and I use FIX to remove the noisy components. When I check my motion parameters before and after FIX, there is a huge difference. A good thing is that I don't need to exclude any of my participants based on their FDafter denoising. However, I was wondering if it's better to have stringent exclusion criteria based on FD before denoising. Should I exclude participants with high motion first and denoise the rest only. Thanks for your help. Sara ________________________________ To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Head of Analysis, WIN (FMRIB) Oxford FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 610470 [log in to unmask]<mailto:[log in to unmask]> http://www.fmrib.ox.ac.uk/~steve --------------------------------------------------------------------------- Stop the cultural destruction of Tibet<http://smithinks.net> ________________________________ To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. 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