Glad you got it all figured out. I’m curious though: was this exercise just to understand the various steps internal to FIX (and hcp_fix) or is there some more fundamental reason that you can't use those actual scripts for your processing?
cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: [email protected] From: <[email protected]<mailto:[email protected]>> on behalf of "Ely, Benjamin" <[email protected]<mailto:[email protected]>> Date: Tuesday, October 4, 2016 at 1:07 AM To: "Burgess, Gregory" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] MELODIC denoising vs. released ICA-FIX datasets Hi Greg, Thank you very much for your detailed response! I have now generated a Movement_Regressors.mat file with the correct 24 parameters (6 rigid body, 6 derivatives, 6 rigid body squared, 6 derivatives squared). As I didn't have code handy to run highpass filtering on the movement regressors, I based this file on the detrended movement regressors; the HCP's highpass filtering is described as "detrending-like", so this should (hopefully) give approximately the same result. I also noticed an error in my original highpass filtering of the fMRI data that accounts for part of the difference I was seeing; the correct sigma is 1389, not 1000 (cutoff = 2*TR*sigma, so a TR of 0.72s and cutoff of 2000s requires a sigma of 1389; I forgot to account for the TR in my original filtering). Between the two, I am able to get much closer to matching the HCP's denoised data. Regarding your second point, I think my setup is removing all of the variance in the movement parameters, but not in the noise ICs. fsl_glm, which is how I remove the movement parameters, appears to always do full regression. By default, though, fsl_regfilt performs partial regression of the specified noise ICs. But the difference regarding movement regression would definitely make a difference and seems to be one thing that can't be matched using FSL only. So yes, this was very informative! Thank you again for your help. -Ely _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ 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. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
