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
