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) [email protected] http://www.fmrib.ox.ac.uk/~steve ---------------------- > On 24 Nov 2015, at 19:03, Greg Burgess <[email protected]> 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: [email protected] > >> On Nov 24, 2015, at 12:29 PM, Glasser, Matthew <[email protected]> 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 <[email protected]> >> Sent: Tuesday, November 24, 2015 11:55 AM >> To: Glasser, Matthew >> Cc: Greg Burgess; Elam, Jennifer; [email protected] >> 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 <[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. >> >> >> 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 _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
