Hi Ely - one additoinal point - if you are wanting to apply these pipelines to your own data, you may want to change the (very unaggressive, basically just detrending as you said) approach to highpass filtering (both in general and for use pre-FIX). I haven't seen many datasets where the "slow" temporal stability is as good as we got in HCP, so typically I would expect a shorter highpass cutoff to be useful.
Cheers. > On 4 Oct 2016, at 07:07, Ely, Benjamin <benjamin....@mssm.edu> wrote: > > 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 > HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Head of Analysis, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) st...@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve> --------------------------------------------------------------------------- Stop the cultural destruction of Tibet <http://smithinks.net/> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
