Skip to content
master
Switch branches/tags
Code

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.

Economics of Connectomics

Code for the paper, Efficient Coding in the Economics of Human Brain Connectomics.

Setup

platform       x86_64-pc-linux-gnu         
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           

language       R                           
version        R version 3.5.1 (2018-07-02)

MATLAB:        8.4.0.150421 (R2014b)

Functions

Download the Brain Connectivity Toolbox

Download polyfix

Download spin test

Download GenLouvain

Move to /scripts/

Author

Dale Zhou (dalezhou [at] pennmedicine.upenn.edu)

Project Organization


    ├── data                                    <- Data goes here.
    ├── figures                                 <- Figures for manuscript.
    │   ├── fig1                   
    │   ├── fig2
    │   ├── fig3
    │   ├── fig4
    │   ├── fig5
    │   ├── fig6
    │   ├── fig7
    │   ├── fig8
    │   ├── supplement
    │ 
    ├── scripts                                 <- Downloaded functions go here
    │
    ├── fig1.R                                  <- CBF vs CMRGlu.
    ├── fig2.R                                  <- CBF of paths.
    ├── fig3.R                                  <- CBF/network structure trade-offs.
    ├── fig4_randomVsBrainRD.m                  <- Rate-distortion function.
    ├── fig4.R                                  <- Compression eff vs age*sex.
    ├── fig5_resourceEfficiencyConcatenate.R    <- Send/rcv compression eff.
    ├── fig5_fitRD.m                            <- Individual compression eff.
    ├── fig5.R                                  <- Random walk vs chemotaxis.
    ├── fig6.R                                  <- High & low fidelity regimes.
    ├── fig7.R                                  <- Send/rcv vs scaling, myelin.
    ├── fig7_atlasCorrelations.m                <- Spin test for spatial corr.
    ├── fig8_preprocessRegional.m               <- Regional send/recv compression eff.
    ├── fig8.R                                  <- Rich-club hubs & speed-accuracy.
    ├── resource_efficiency_wei.m               <- Resource efficiency for WU networks.
    ├── supplement_richClubCBF.R                <- CBF of rich-club vs non-rich-club.
    ├── supplement_subnetworks.R                <- Yeo 7 subnetwork levels.
    │
    ├── README.md

Order of scripts

  1. fig1.R
  2. fig2.R
  3. fig3.R
  4. fig4.R
  5. fig4_randomVsBrainRD.m
  6. fig5_resourceEfficiencyConcatenate.R
  7. fig5_fitRD.m
  8. fig5.R
  9. fig6.R
  10. fig7.R
  11. fig7_atlasCorrelations.m
  12. fig8_preprocessRegional.m
  13. fig8.R
  14. supplement_richClubCBF.R
  15. supplement_subnetworks.R

Notes

Will need cluster for extra memory for some of these steps, such as Fig 2.

qlogin -q qlogin.himem.q -l h_vmem=15G,s_vmem=15G

About

Code for the paper "Efficient Coding in the Economics of Human Brain Connectomics"

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published