I suggested below that Joelle could average Fisher’s z-transformed correlation coefficients (derived from each run within-subject), or treat the multiple runs as within-subjects repeated measures.
The idea was that computing correlations between timeseries with 4800 time points will take four times as much RAM as using only 1200 time points. For folks with limited RAM, averaging the correlation estimates may be a more feasible option. --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 1:08 PM, Stephen Smith <st...@fmrib.ox.ac.uk> wrote: > > I think maybe we need to be explicit about exactly what we're talking about > averaging? > Cheers. > > -------------------- > Stephen M. Smith, Professor of Biomedical Engineering > Head of Analysis, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, > Oxford. OX3 9 DU, UK > +44 (0) 1865 222726 (fax 222717) > st...@fmrib.ox.ac.uk > http://www.fmrib.ox.ac.uk/~steve > ---------------------- > >> On 24 Nov 2015, at 19:03, Greg Burgess <gcburg...@gmail.com> wrote: >> >> 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 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
