urgh - yes you're right.
> On 16 Feb 2015, at 16:47, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: > > Also to Steve: if these are used after ICA+FIX, don’t they need to have the > 24 motion parameters and noise ICA component timeseries confounds regressed > out as well, before being used on the cleaned data? > > Peace, > > Matt. > > From: <Harms>, Michael <mha...@wustl.edu <mailto:mha...@wustl.edu>> > Date: Monday, February 16, 2015 at 10:42 AM > To: Matt Glasser <glass...@wusm.wustl.edu <mailto:glass...@wusm.wustl.edu>>, > Stephen Smith <st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>>, Miriam > Klein-Flügge <miriam.klein-flu...@psy.ox.ac.uk > <mailto:miriam.klein-flu...@psy.ox.ac.uk>> > Cc: "hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>" > <hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>> > Subject: Re: [HCP-Users] Incorporating physiological monitoring data > > > Not only that, but just because a given physiological trace exists, doesn't > necessarily mean that it is a *good* trace. There is going to be > considerable variability in the quality of the physiological measurements, > which presents a challenge in using them in a large scale study. I'm sure > that Greg will comment more when he has a chance. > > 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: mha...@wustl.edu <mailto:mha...@wustl.edu> > > From: <Glasser>, Matt Glasser <glass...@wusm.wustl.edu > <mailto:glass...@wusm.wustl.edu>> > Date: Monday, February 16, 2015 10:10 AM > To: Stephen Smith <st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>>, > Miriam Klein-Flügge <miriam.klein-flu...@psy.ox.ac.uk > <mailto:miriam.klein-flu...@psy.ox.ac.uk>> > Cc: "hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>" > <hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>> > Subject: Re: [HCP-Users] Incorporating physiological monitoring data > > Note that a major reason we didn’t use these physiological confound > regressors was they don’t exist for every subject, so be sure to select a > subset of subjects that have them. We’d also be interested to know if you > found they were helpful. > > Peace, > > Matt. > > From: Stephen Smith <st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>> > Date: Monday, February 16, 2015 at 8:05 AM > To: Miriam Klein-Flügge <miriam.klein-flu...@psy.ox.ac.uk > <mailto:miriam.klein-flu...@psy.ox.ac.uk>> > Cc: "hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>" > <hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>> > Subject: Re: [HCP-Users] Incorporating physiological monitoring data > > Hi - I think you would probably be best off taking the FIX-cleaned version of > the data, and then apply additional confound regressors if they will help. > Don't forget to apply the same highpass filter (to those regressors) that was > applied already in the data preproc, before you use them. > > Cheers. > > > >> On 16 Feb 2015, at 13:35, Miriam Klein-Flügge >> <miriam.klein-flu...@psy.ox.ac.uk <mailto:miriam.klein-flu...@psy.ox.ac.uk>> >> wrote: >> >> Dear all, >> Is it correct that until now the physiological monitoring data is not made >> use of in the preprocessing of the rfMRI data? I would like to correct for >> cardiac and respiratory signals and wondered how to best do that. I can see >> that FIX-denoising probably takes care of this type of noise but I am >> particularly interested in looking at the brain stem and in my experience, >> including physiological regressors in the preprocessing makes a big >> difference there. >> Would you recommend using the spatially (minimally) pre-processed rfMRI >> data, performing the high-pass filtering on it myself and then incorporating >> the physiological regressors at that stage, or is there a better stage at >> which to do it? Also, is there a standard procedure for regressing out the >> physiological regressors that you can recommend? >> Many thanks in advance! >> Kind regards, >> Miriam >> -- >> Miriam Klein-Flügge >> Sir Henry Wellcome Postdoctoral Fellow >> Department of Experimental Psychology >> University of Oxford >> >> _______________________________________________ >> 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 > Associate Director, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 (fax 222717) > st...@fmrib.ox.ac.uk <mailto: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 <mailto:HCP-Users@humanconnectome.org> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <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 > 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> > > > 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. --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, 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
