Skip to content
Code for the paper "Efficient Coding in the Economics of Human Brain Connectomics"
R MATLAB
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
data
figures
scripts
README.md
fig1.R
fig2.R
fig3.R
fig4.R
fig4_randomVsBrainRD.m
fig5.R
fig5_fitRD.m
fig5_preprocessResourceEfficiencyReceive.m
fig5_preprocessResourceEfficiencySend.m
fig5_resourceEfficiencyConcatenate.R
fig6.R
fig7.R
fig7_atlasCorrelations.m
fig8.R
fig8_preprocessRegional.m
resource_efficiency_wei.m
supplement_richClubCBF.R
supplement_subnetworks.R

README.md

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

You can’t perform that action at this time.