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 Email: [email protected] > On Nov 23, 2015, at 4:40 PM, Glasser, Matthew <[email protected]> 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: <[email protected]> on behalf of Joelle Zimmermann > <[email protected]> > Date: Monday, November 23, 2015 at 12:48 PM > To: "Elam, Jennifer" <[email protected]> > Cc: "[email protected]" <[email protected]> > 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 <[email protected]> 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 >> [email protected] >> www.humanconnectome.org >> >> From:[email protected] >> [mailto:[email protected]] On Behalf Of Glasser, Matthew >> Sent: Monday, November 23, 2015 12:16 PM >> To: Joelle Zimmermann; [email protected] >> 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:[email protected] >> <[email protected]> on behalf of Joelle Zimmermann >> <[email protected]> >> Sent: Monday, November 23, 2015 11:33 AM >> To: [email protected] >> 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 >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
