It’s less RAM-intensive since you only need to load one timeseries at a time.
--Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology Phone: 314-362-7864 Email: gburg...@wustl.edu > On Nov 24, 2015, at 12:29 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > > I'm not sure what benefit you'd get from averaging the FCs across runs within > a subject. That just sounds more computationally intensive. > > Peace, > > Matt. > > > From: Joelle Zimmermann <joelle.t.zimmerm...@gmail.com> > Sent: Tuesday, November 24, 2015 11:55 AM > To: Glasser, Matthew > Cc: Greg Burgess; Elam, Jennifer; hcp-users@humanconnectome.org > Subject: Re: [HCP-Users] Phase Encoding left-to-right and right-to-left > > Hi Matt, > > Glad you do point that out, because I was previously looking at the Resting > State fMRI 1 Preprocessed, but the Resting State fMRI FIX-Denoised (Compact) > is readily available. So I guess for that all I'll need to do is demean and > variance normalize, and/or average the two FCs. > > Thanks, > Joelle > > On Tue, Nov 24, 2015 at 12:19 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > Indeed I was assuming you were using FIX cleaned data. I wouldn't recommend > not using FIX cleaned data unless you are testing other clean up approaches. > > Peace, > > Matt. > ________________________________________ > From: Joelle Zimmermann [joelle.t.zimmerm...@gmail.com] > Sent: Tuesday, November 24, 2015 11:14 AM > To: Greg Burgess > Cc: Glasser, Matthew; Elam, Jennifer; hcp-users@humanconnectome.org > Subject: Re: [HCP-Users] Phase Encoding left-to-right and right-to-left > > Hi Greg, > > Thanks for your response. Indeed, I was considering that myself, to compute > the FCs separately and average the LR and RL. > > Thanks, > Joelle > > On Tue, Nov 24, 2015 at 11:56 AM, Greg Burgess > <gcburg...@gmail.com<mailto:gcburg...@gmail.com>> wrote: > Hi Joelle, > > In addition to demeaning and possibly variance normalization, it is probably > a good idea to detrend each run separately using a linear detrend or a high > pass filter before concatenation. (FIX-preprocessed data already includes a > 2000s high pass filter.) > > Another option that is not described on the wiki (yet) is to compute > correlations separately for each run, and then average the Fisher’s > z-transformed correlation coefficients, or treat the multiple runs as > within-subjects repeated measures. > > --Greg > > ____________________________________________________________________ > Greg Burgess, Ph.D. > Staff Scientist, Human Connectome Project > Washington University School of Medicine > Department of Anatomy and Neurobiology > Phone: 314-362-7864<tel:314-362-7864> > Email: gburg...@wustl.edu<mailto:gburg...@wustl.edu> > > > On Nov 23, 2015, at 4:40 PM, Glasser, Matthew > > <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: > > > > It doesn’t matter what order you concatenate the data in, but I would not > > recommend only analyzing the data of one phase encoding direction. > > > > Peace, > > > > Matt. > > > > From: > > <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> > > on behalf of Joelle Zimmermann > > <joelle.t.zimmerm...@gmail.com<mailto:joelle.t.zimmerm...@gmail.com>> > > Date: Monday, November 23, 2015 at 12:48 PM > > To: "Elam, Jennifer" <e...@wustl.edu<mailto:e...@wustl.edu>> > > Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" > > <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> > > Subject: Re: [HCP-Users] Phase Encoding left-to-right and right-to-left > > > > Hi Jennifer and Matt, > > > > Thanks for your help. I have a few clarification questions below: > > Does it matter in which order I concatenate the LR and the RL .nii's? My > > ultimate goal is to create a functional connectivity matrix from the time > > series. > > #3 in the link you sent describes that there are 4 runs per subject. Is > > this the REST 1, and REST 2, each with LR and RL phase encoding directions? > > Would using only one phase encoding direction (i.e. do analysis on LR) > > expect to effect the results? > > > > Thanks, > > Joelle > > > > On Mon, Nov 23, 2015 at 1:17 PM, Jennifer Elam > > <el...@pcg.wustl.edu<mailto:el...@pcg.wustl.edu>> wrote: > >> #3 on https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ > >> may be of help. > >> > >> Best, > >> Jenn > >> > >> Jennifer Elam, Ph.D. > >> Outreach Coordinator, Human Connectome Project > >> Washington University School of Medicine > >> Department of Anatomy and Neurobiology, Box 8108 > >> 660 South Euclid Avenue > >> St. Louis, MO 63110 > >> 314-362-9387<tel:314-362-9387> > >> el...@pcg.wustl.edu<mailto:el...@pcg.wustl.edu> > >> www.humanconnectome.org<http://www.humanconnectome.org> > >> > >> From:hcp-users-boun...@humanconnectome.org<mailto:from%3ahcp-users-boun...@humanconnectome.org> > >> > >> [mailto:hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>] > >> On Behalf Of Glasser, Matthew > >> Sent: Monday, November 23, 2015 12:16 PM > >> To: Joelle Zimmermann; > >> hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> > >> Subject: Re: [HCP-Users] Phase Encoding left-to-right and right-to-left > >> > >> > >> > >> Usually you concatenate them temporally after demeaning (and perhaps > >> variance normalizing). > >> > >> > >> > >> Peace, > >> > >> > >> > >> Matt. > >> > >> > >> > >> From:hcp-users-boun...@humanconnectome.org<mailto:from%3ahcp-users-boun...@humanconnectome.org> > >> > >> <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> > >> on behalf of Joelle Zimmermann > >> <joelle.t.zimmerm...@gmail.com<mailto:joelle.t.zimmerm...@gmail.com>> > >> Sent: Monday, November 23, 2015 11:33 AM > >> To: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> > >> Subject: [HCP-Users] Phase Encoding left-to-right and right-to-left > >> > >> > >> > >> Hi all, > >> > >> > >> > >> Would anyone be able to explain a bit more about the phase-encoding > >> directions LR and RL for the (preprocessed) REST1 session data from 500 > >> subjects +MEG2? I understand that LR is left to right and RL is right to > >> left. > >> > >> > >> > >> I'm wondering, are these meant to be somehow combined, or is only one of > >> these typically chosen? > >> > >> > >> > >> Thanks, > >> > >> Joelle > >> > >> > >> > >> > >> > >> http://www.humanconnectome.org/documentation/Q1/data-in-this-release.html > >> > >> Q1 Data Release: About the Dataset | Human Connectome Project > >> 76 healthy adult subjects in the age range 22 – 35 participated in the > >> first quarter of data collection. These include 68 subjects with data from > >> all or nearly all ... > >> Read more... > >> > >> > >> _______________________________________________ > >> HCP-Users mailing list > >> HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> > >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users > >> > >> _______________________________________________ > >> HCP-Users mailing list > >> HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> > >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users > >> > > > > _______________________________________________ > > HCP-Users mailing list > > HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > _______________________________________________ > > HCP-Users mailing list > > HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> > > 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. > > > 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 http://lists.humanconnectome.org/mailman/listinfo/hcp-users
