Dear Dr. Harms, Thank you very much for your codes. They are very helpful for me to understand how FSLNets works. I am able to reproduce individual netmats that are perfectly correlated with HCP distributed netmats.
I also tried the mean netmat of full correlations netmats from the 4 runs. They also give me netmats that are perfectly correlated with HCP distributed netmats (by perfectly correlated I mean Pearson's correlation=1.0000 in matlab). Thus the AR(1) process does not seem to affect the result very much. Since I still do not understand the scaling of the z values in HCP distributed netmats, may I know how I can transform them back to r values, so that to get an idea of the size of correlation? (to run nets_netmats with z=0 (leave netmats as r)) is too time consuming for this purpose). Thanks, Cherry On Mon, Mar 30, 2015 at 1:34 PM, Harms, Michael <[email protected]> wrote: > > Hi, > You'll want to refer to the relevant functions in the FSLnets package. > > I did something very similar to what you are trying to do recently. > Here is the code that you want to use if you are trying to replicate the > distributed netmats (pconn's) from the distributed time-series: > > ts_dir='PATH_TO_TIMESERIES'; > nRuns = 4; > ts = nets_load(ts_dir,0.72,1,nRuns); > netmat1 = nets_netmats(ts,1,'corr'); > > Of note, the estimation of the AR(1) correction factor that is used > internally in nets_netmats as part of the r-to-z transformation is the > median over all subjects, so if you are trying to duplicate the HCP > distributed netmats "exactly", you correspondingly need to load the full > set of distributed time-series as part of your 'nets_load' command. Even > then, there will be a very small residual difference in the resulting > output from nets_netmats due to the random seed component of the AR(1) > simulation (i.e., running nets_netmats twice does not itself generate > identical results when using its r-to-z conversion option). > > 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: Yizhou Ma <[email protected]> > Date: Monday, March 30, 2015 12:26 PM > To: Stephen Smith <[email protected]> > > Cc: "[email protected]" <[email protected]> > Subject: Re: [HCP-Users] netmats in HCP > > Thank you all. I don't see a comment on correction for temporal > autocorrelation in the PTN document though. Could someone please point me > to a page where this is explained? > > Thanks, > Cherry > > On Mon, Mar 30, 2015 at 12:18 PM, Stephen Smith <[email protected]> > wrote: > >> yup - that also affects the scaling - see FSLNets doc and the PTN release >> doc. >> Cheers. >> >> >> On 30 Mar 2015, at 18:17, Glasser, Matthew <[email protected]> >> wrote: >> >> Hi Steve, >> >> What about the correction for temporal autocorrelation? >> >> Matt. >> >> From: Stephen Smith <[email protected]> >> Date: Monday, March 30, 2015 at 12:15 PM >> To: Yizhou Ma <[email protected]> >> Cc: "[email protected]" <[email protected]> >> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 >>>> [email protected] >>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> >>> >>> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> 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) >> [email protected] 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 >> >> >> ------------------------------ >> 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) >> [email protected] 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 > > > ------------------------------ > > 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
