yup - that also affects the scaling - see FSLNets doc and the PTN release doc. Cheers.
> On 30 Mar 2015, at 18:17, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: > > Hi Steve, > > What about the correction for temporal autocorrelation? > > Matt. > > From: Stephen Smith <st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>> > Date: Monday, March 30, 2015 at 12:15 PM > To: Yizhou Ma <maxxx...@umn.edu <mailto:maxxx...@umn.edu>> > Cc: "hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>" > <hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>> > Subject: Re: [HCP-Users] netmats in HCP > > Hi - one thing is that we estimate (z versions of) netmats separately for > each 15min run and then average the 4 netmats to give a single netmat per > subject. > Cheers. > > >> On 30 Mar 2015, at 18:14, Yizhou Ma <maxxx...@umn.edu >> <mailto:maxxx...@umn.edu>> wrote: >> >> Hi Timothy, >> >> Thank you for pointing that out. I typed that wrong but I used the correct >> transformation in matlab. As I said my transformed z scores are actually >> almost perfectly linearly correlated with HCP netmats, though the latter is >> much larger. I want to understand why the latter is larger and why the two >> are not exactly correlated. >> >> Thanks, >> Cherry >> >> On Mon, Mar 30, 2015 at 12:08 PM, Timothy Coalson <tsc...@mst.edu >> <mailto:tsc...@mst.edu>> wrote: >>> A quick possibility: if you have pasted in the formula you used, I see an >>> order of operations problem: .5*ln(1+r)-ln(1-r) means (.5*ln(1+r))-ln(1-r), >>> where the usual formula is .5*ln((1+r)/(1-r)), which after some log >>> identities becomes .5*(ln(1+r)-ln(1-r)). >>> >>> Tim >>> >>> >>> On Mon, Mar 30, 2015 at 11:02 AM, Yizhou Ma <maxxx...@umn.edu >>> <mailto:maxxx...@umn.edu>> wrote: >>>> Dear HCP experts, >>>> >>>> I am trying to reproduce the individual netmats from HCP500-PTN so that I >>>> am sure where the numbers come from. I used individual node timeseries in >>>> /ts2/subjID and did correlation in matlab. I then used fisher's z >>>> transformation: .5*ln(1+r)-ln(1-r). The resulting netmat is different from >>>> what is provided in *_netmat1/. However, they almost have a linear >>>> relationship. It seems to me that HCP is not using the same z >>>> transformation I have used. The transformation seems more like >>>> 7*ln(1+r)-ln(1-r). >>>> >>>> I have downloaded FSLNets but could not identify which function was used >>>> to generate individual netmats in the first place. The example script >>>> seems to be about group-level netmats only. >>>> >>>> Could you please share with me how exactly the numbers in individual >>>> netmats were generated? >>>> >>>> Thanks, >>>> Cherry >>>> _______________________________________________ >>>> HCP-Users mailing list >>>> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org> >>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> <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 >> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> > > --------------------------------------------------------------------------- > Stephen M. Smith, Professor of Biomedical Engineering > Associate Director, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 (fax 222717) > st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk> > 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 > HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org> > 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. --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) st...@fmrib.ox.ac.uk 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
