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 <[email protected]> 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 [[email protected]] > Sent: Tuesday, November 24, 2015 11:14 AM > To: Greg Burgess > Cc: Glasser, Matthew; Elam, Jennifer; [email protected] > 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 <[email protected] > <mailto:[email protected]>> 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: [email protected]<mailto:[email protected]> > > > On Nov 23, 2015, at 4:40 PM, Glasser, Matthew <[email protected] > <mailto:[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]<mailto: > [email protected]>> on behalf of Joelle Zimmermann < > [email protected]<mailto:[email protected]>> > > Date: Monday, November 23, 2015 at 12:48 PM > > To: "Elam, Jennifer" <[email protected]<mailto:[email protected]>> > > Cc: "[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[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] > <mailto:[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<tel:314-362-9387> > >> [email protected]<mailto:[email protected]> > >> www.humanconnectome.org<http://www.humanconnectome.org> > >> > >> From:[email protected]<mailto: > from%[email protected]> [mailto: > [email protected]<mailto: > [email protected]>] On Behalf Of Glasser, Matthew > >> Sent: Monday, November 23, 2015 12:16 PM > >> To: Joelle Zimmermann; [email protected]<mailto: > [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]<mailto: > from%[email protected]> < > [email protected]<mailto: > [email protected]>> on behalf of Joelle Zimmermann < > [email protected]<mailto:[email protected]>> > >> Sent: Monday, November 23, 2015 11:33 AM > >> To: [email protected]<mailto:[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]<mailto:[email protected]> > >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users > >> > >> _______________________________________________ > >> HCP-Users mailing list > >> [email protected]<mailto:[email protected]> > >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users > >> > > > > _______________________________________________ > > HCP-Users mailing list > > [email protected]<mailto:[email protected]> > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > _______________________________________________ > > HCP-Users mailing list > > [email protected]<mailto:[email protected]> > > 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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
