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:
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- [HCP-Users] netmats in HCP Yizhou Ma
- Re: [HCP-Users] netmats in HCP Timothy Coalson
- Re: [HCP-Users] netmats in HCP Yizhou Ma
- Re: [HCP-Users] netmats in HCP Stephen Smith
- Re: [HCP-Users] netmats in HCP Glasser, Matthew
- Re: [HCP-Users] netmats in HCP Stephen Smith
- Re: [HCP-Users] netmats in HCP Yizhou Ma
- Re: [HCP-Users] netmats in ... Harms, Michael
- Re: [HCP-Users] netmats in ... Yizhou Ma
- Re: [HCP-Users] netmats in ... Harms, Michael
- Re: [HCP-Users] netmats in ... Yizhou Ma