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<mailto: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<mailto: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<mailto: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><mailto: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><tel:314-362-7864<tel:314-362-7864>> Email: gburg...@wustl.edu<mailto:gburg...@wustl.edu><mailto:gburg...@wustl.edu<mailto:gburg...@wustl.edu>> > On Nov 23, 2015, at 4:40 PM, Glasser, Matthew > <glass...@wustl.edu<mailto:glass...@wustl.edu><mailto: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><mailto: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><mailto: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><mailto:e...@wustl.edu<mailto:e...@wustl.edu>>> > Cc: > "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org><mailto:hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>" > > <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org><mailto: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><mailto: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><tel:314-362-9387<tel:314-362-9387>> >> el...@pcg.wustl.edu<mailto:el...@pcg.wustl.edu><mailto:el...@pcg.wustl.edu<mailto:el...@pcg.wustl.edu>> >> www.humanconnectome.org<http://www.humanconnectome.org><http://www.humanconnectome.org> >> >> From:hcp-users-boun...@humanconnectome.org<mailto:from%3ahcp-users-boun...@humanconnectome.org><mailto:from%3ahcp-users-boun...@humanconnectome.org<mailto:from%253ahcp-users-boun...@humanconnectome.org>> >> >> [mailto:hcp-users-boun...@humanconnectome.org<mailto:hcp-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><mailto: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><mailto:from%3ahcp-users-boun...@humanconnectome.org<mailto:from%253ahcp-users-boun...@humanconnectome.org>> >> >> <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org><mailto: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><mailto: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><mailto: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><mailto: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><mailto: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><mailto: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><mailto: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. 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