Re: [HCP-Users] netmats in HCP

[Harms, Michael]

The AR(1) correction is a scaling applied during the r-to-z transformation This is from nets_netmats.m RtoZcorrection=1/std(grotZ); netmats=0.5*log((1+netmats)./(1-netmats))*RtoZcorrection; So, if you knew the value of RtoZcorrection you could convert the HCP distributed netmats back to r-value.  BUT, that value wasn't saved. If you want the netmats expressed as correlations (r-values) why not just run: ts_dir='PATH_TO_TIMESERIES'; nRuns = 4; ts = nets_load(ts_dir,0.72,1,nRuns); netmat1 = nets_netmats(ts,0,'corr');  %% Second argument 0, to leave netmats as r It takes a little bit of time, but not *that* much, and you only need to do it once.  If I recall correctly, when I did it on the full set of time-series from the HCP 500 release, it took something like an hour or two total for the nets_load and nets_netmats steps. 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: mha...@wustl.edu From: Yizhou Ma <maxxx...@umn.edu> Date: Monday, March 30, 2015 6:54 PM To: "Harms, Michael" <mha...@wustl.edu> Cc: Stephen Smith <st...@fmrib.ox.ac.uk>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] netmats in HCP 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 <mha...@wustl.edu> 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: mha...@wustl.edu From: Yizhou Ma <maxxx...@umn.edu> Date: Monday, March 30, 2015 12:26 PM To: Stephen Smith <st...@fmrib.ox.ac.uk> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> 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 <st...@fmrib.ox.ac.uk> 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 <glass...@wusm.wustl.edu> wrote: Hi Steve, What about the correction for temporal autocorrelation? Matt. From: Stephen Smith <st...@fmrib.ox.ac.uk> Date: Monday, March 30, 2015 at 12:15 PM To: Yizhou Ma <maxxx...@umn.edu> Cc: "hcp-users@humanconnectome.org" <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> 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> 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> 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 http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org 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    http://www.fmrib.ox.ac.uk/~steve --------------------------------------------------------------------------- Stop the cultural destruction of Tibet _______________________________________________ HCP-Users mailing list 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. --------------------------------------------------------------------------- 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 --------------------------------------------------------------------------- Stop the cultural destruction of Tibet _______________________________________________ HCP-Users mailing list 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