Re: [HCP-Users] netmats in HCP

[Glasser, Matthew]

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. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users