Hi Michael - for raw covariances - summing covariances is equivalent to temp concat first. Cheers
> On 25 Nov 2015, at 17:29, Harms, Michael <[email protected]> wrote: > > > To Steve's point and the issue of memory: A critical distinction is whether > you are intending to work with dense connectomes or parcellated connectomes. > In the context of parcellated connectomes, both Steve and myself have found a > small advantage in reproducibility if you compute a parcellated "netmat" for > each resting state run, convert those using r-to-z, and then average those > across the 4 resting state runs for a subject (if you want as output a single > parcellated netmat per subject). In fact, that is how the netmats that are > distributed as part of the "PTN" from ConnectomeDB were themselves created. > > In the context of dense connectomes, generating a dense connectome per run is > a different sort of beast. You can do it (I've done it) using > -cifti-correlation and then average with -cifti-average. But to my knowledge, > no one has looked at whether there is a small reproducibility advantage to > that approach as well with dense connectomes, which is why I think that most > subject specific dense connectomes have probably been created via the > 'concat' approach outlined on the wiki. > > cheers, > -MH > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: [email protected] > > From: Timothy Coalson <[email protected] <mailto:[email protected]>> > Date: Tuesday, November 24, 2015 4:23 PM > To: Greg Burgess <[email protected] <mailto:[email protected]>> > Cc: "Elam, Jennifer" <[email protected] <mailto:[email protected]>>, > "[email protected] <mailto:[email protected]>" > <[email protected] <mailto:[email protected]>> > Subject: Re: [HCP-Users] Phase Encoding left-to-right and right-to-left > > If you are using -cifti-correlation, there is a -mem-limit option for this > purpose, so there isn't a required minimum memory to do it (even in matlab > where everything has to be in memory, the 90k x 4.8k timeseries input pales > in comparison to the 90k x 90k output). If you are doing everything in > matlab, then the averaging of two 90k x 90k dconns is going to require more > memory than any reasonable concatenated correlation. > > The -cifti-average command should use almost no memory regardless of file > size, as long as you don't overwrite one of the inputs with the output. > > Tim > > > On Tue, Nov 24, 2015 at 2:23 PM, Greg Burgess <[email protected] > <mailto:[email protected]>> wrote: >> 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 <tel:314-362-7864> >> Email: [email protected] <mailto:[email protected]> >> >> > On Nov 24, 2015, at 1:08 PM, Stephen Smith <[email protected] >> > <mailto:[email protected]>> 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 <tel:%2B44%20%280%29%201865%20222726> (fax 222717) >> > [email protected] <mailto:[email protected]> >> > http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve> >> > ---------------------- >> > >> >> On 24 Nov 2015, at 19:03, Greg Burgess <[email protected] >> >> <mailto:[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 <tel:314-362-7864> >> >> Email: [email protected] <mailto:[email protected]> >> >> >> >>> On Nov 24, 2015, at 12:29 PM, Glasser, Matthew <[email protected] >> >>> <mailto:[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] >> >>> <mailto:[email protected]>> >> >>> Sent: Tuesday, November 24, 2015 11:55 AM >> >>> To: Glasser, Matthew >> >>> Cc: Greg Burgess; Elam, Jennifer; [email protected] >> >>> <mailto:[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] >> >>> <mailto:[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] >> >>> <mailto:[email protected]>] >> >>> Sent: Tuesday, November 24, 2015 11:14 AM >> >>> To: Greg Burgess >> >>> Cc: Glasser, Matthew; Elam, Jennifer; [email protected] >> >>> <mailto:[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]><mailto:[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><tel:314-362-7864 >> >>> <tel:314-362-7864>> >> >>> Email: [email protected] >> >>> <mailto:[email protected]><mailto:[email protected] >> >>> <mailto:[email protected]>> >> >>> >> >>>> On Nov 23, 2015, at 4:40 PM, Glasser, Matthew <[email protected] >> >>>> <mailto:[email protected]><mailto:[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]><mailto:[email protected] >> >>>> <mailto:[email protected]>>> on behalf of Joelle >> >>>> Zimmermann <[email protected] >> >>>> <mailto:[email protected]><mailto:[email protected] >> >>>> <mailto:[email protected]>>> >> >>>> Date: Monday, November 23, 2015 at 12:48 PM >> >>>> To: "Elam, Jennifer" <[email protected] >> >>>> <mailto:[email protected]><mailto:[email protected] <mailto:[email protected]>>> >> >>>> Cc: "[email protected] >> >>>> <mailto:[email protected]><mailto:[email protected] >> >>>> <mailto:[email protected]>>" >> >>>> <[email protected] >> >>>> <mailto:[email protected]><mailto:[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]><mailto:[email protected] >> >>>>> <mailto:[email protected]>>> wrote: >> >>>>> #3 on >> >>>>> https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ >> >>>>> <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><tel:314-362-9387 <tel:314-362-9387>> >> >>>>> [email protected] >> >>>>> <mailto:[email protected]><mailto:[email protected] >> >>>>> <mailto:[email protected]>> >> >>>>> www.humanconnectome.org >> >>>>> <http://www.humanconnectome.org/><http://www.humanconnectome.org >> >>>>> <http://www.humanconnectome.org/>> >> >>>>> >> >>>>> From:[email protected] >> >>>>> <mailto:from%[email protected]><mailto:from%[email protected] >> >>>>> <mailto:from%[email protected]>> >> >>>>> [mailto:[email protected] >> >>>>> <mailto:[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]><mailto:[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]><mailto:from%[email protected] >> >>>>> <mailto:from%[email protected]>> >> >>>>> <[email protected] >> >>>>> <mailto:[email protected]><mailto:[email protected] >> >>>>> <mailto:[email protected]>>> on behalf of Joelle >> >>>>> Zimmermann <[email protected] >> >>>>> <mailto:[email protected]><mailto:[email protected] >> >>>>> <mailto:[email protected]>>> >> >>>>> Sent: Monday, November 23, 2015 11:33 AM >> >>>>> To: [email protected] >> >>>>> <mailto:[email protected]><mailto:[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 >> >>>>> >> >>>>> <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]><mailto:[email protected] >> >>>>> <mailto:[email protected]>> >> >>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >>>>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> >> >>>>> >> >>>>> _______________________________________________ >> >>>>> HCP-Users mailing list >> >>>>> [email protected] >> >>>>> <mailto:[email protected]><mailto:[email protected] >> >>>>> <mailto:[email protected]>> >> >>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >>>>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> >> >>>> >> >>>> _______________________________________________ >> >>>> HCP-Users mailing list >> >>>> [email protected] >> >>>> <mailto:[email protected]><mailto:[email protected] >> >>>> <mailto:[email protected]>> >> >>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >>>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> >> >>>> _______________________________________________ >> >>>> HCP-Users mailing list >> >>>> [email protected] >> >>>> <mailto:[email protected]><mailto:[email protected] >> >>>> <mailto:[email protected]>> >> >>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >>>> <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] <mailto:[email protected]> >> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> <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 >> <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 > <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. 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Smith, Professor of Biomedical Engineering Head of Analysis, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [email protected] http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve> --------------------------------------------------------------------------- Stop the cultural destruction of Tibet <http://smithinks.net/> _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
