README.md

MATLAB Connectome Intro

Developed by Stuart Oldham Instructions for getting started with MATLAB on our cluster.

Getting Started

• Make sure you can log in to MASSIVE
• Make sure you have created your own folder in kg98/scratch i.e. /home/XXXX0001/kg98_scratch/MYNAME ('personal folder')

Installing Software

• Go to your personal folder > right click > 'Open in Terminal'
• Install some of the lab's libraries
  • Type git clone https://github.com/BMHLab/MATLAB-connectome-intro
  • Type git clone https://github.com/StuartJO/plotSurfaceROIBoundary
• Open Firefox
• Install the Brain Connectivity Toolbox
  • Download the Brain Connectivity Toolbox from https://drive.google.com/file/d/1DmMvRnferBfGe057O-sZwB5jL4j8w1Hu/view
  • Go to your downloads folder (probably at /home/XXXX0001/Downloads), double click on BCT.zip, click Extract, and extract it into your personal folder)
• Install BrainNet Viewer
  • Download from https://www.nitrc.org/projects/bnv/
  • Extract it to /home/XXXX0001/kg98_scratch/MYNAME/BrainNet_Viewer

Opening MATLAB

• Back to terminal, type cd MATLAB-connectome-intro
• Then type module load matlab/r2019b
• Then type matlab & --> MATLAB will open

Running and Reading Code

• Open MATLAB_connectome_intro.m by double clicking
• Go through each section of code by using the 'Run Section' button.
  • Each section of code in MATLAB is separated by a %% sign at the start of the section.
  • Click into each section (the current section will be highlighted in yellow), and then press the 'Run Section' button in the toolbar at the top (under the 'Editor' panel)
  • Read the comments and the code. Think about each line, and ask your supervisor any questions.