A question about the netmats

[Aaron]

Dear HCP experts,

I have a question about the computation of netmats. I tried the following code from the HCP manual but the results did not completely reproduce the netmats downloaded from db.humanconnectome.org:

netmat2=nets_netmats(ts,1,'ridgep',0.01); % regularised partial correlation  

Is the original code used for calculating netmats available somewhere in the HCP pipeline? Thank you.

[Elam, Jennifer]

Hi Aaron,

The scripts for calculating the netmats downloaded from db.humanconnectome.org should be included in the scripts.tar.gz file in that download (HCP1200_Parcellation_Timeseries_Netmats.zip or HCP1200_Parcellation_Timeseries_Netmats_recon2.zip).

Here's the documentation for that analysis:

https://www.humanconnectome.org/storage/app/media/documentation/s1200/HCP1200-DenseConnectome+PTN+Appendix-July2017.pdf 

If you have other questions, Steve should be able to help you.

Best,

Jenn

Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
el...@wustl.edu
www.humanconnectome.org

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From: Aaron <aaron...@outlook.com>
Sent: Friday, February 12, 2021 11:19 AM
To: HCP-Users <hcp-...@humanconnectome.org>
Subject: [hcp-users] A question about the netmats

 

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[Aaron]

Hi Jennifer,

Thank you for letting me know. I found the code in "scripts.tar.gz". 

It seems that each time when I use the function "nets_netmats" on the same input, the results are slightly different from previous runs.

Is there any random component built into this "nets_netmats" function? I looked into this function but did not quite get it. Thank you.

[Steve Smith]

HI - yes there is a slightly randomised part to just the bit that converts from r to z - as it tries to empirically estimate what the temporal effective degrees of freedom is. See the usage comments at the top of the file for more info, and how to turn this scaling aspect off.

Cheers.

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Stephen M. Smith, Professor of Biomedical Engineering
Head of Analysis,  WIN (FMRIB) Oxford

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 610470
st...@fmrib.ox.ac.uk    http://www.fmrib.ox.ac.uk/~steve

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