The following resources are useful as background and/or for a further dive into the topics discussed in this course:
Here are a number of possible sources of open brain network data for the project:
There are also two neuroscience-specific portals that you can use to search for relevant data:
For this course we will use a virtual machine that will allow everyone to have an identical environment regardless of their operating system. You are of course free to install all of the dependencies on your own system, but they are not guaranteed to work (and some will certainly not work if you are on Windows).
To use the VM, first set up the following software on your computer:
Install VirtualBox
Install Vagrant
Install git if you don’t already have it.
Go to github.com and log into your account. Then go to the class repository:
https://github.com/BrainNetworksCourse/brain-networks-course
Click the Fork button to create a fork of the repository in your github account. This will allow you to make changes and submit them for inclusion in the main repository, and is the standard approach used for collaborative software development on github.
Clone the repository onto your computer:
git clone https://github.com/<your github username>/brain-networks-course.git
inserting your github username in the appropriate place in the URL.
Go into the repo directory and open the file called “vagrant_setup.rb” in your favorite text editor. Change the following line:
GITHUB_USERNAME = "poldrack"
by replacing poldrack with your own github username. Be sure to save the file and then commit it to your fork:
git add vagrant_setup.rb
git commit -m"changing github username"
git push origin master
Run the following command to provision the virtual machine (this will take a little while the first time you do it, and involves lots of downloading so be sure to do it from a good network):
vagrant up
Once the installation is done, then restart the virtual machine; to do this, go to the VirtualBox window for the VM (which should just show a login window), close the VM window, and choose “Power off the machine”. Then run vagrant up again to restart it. At this point, a GUI window should appear for the VM, which we will use for our class exercises.
On occasion we will update the VM with new packages. To pull the latest changes into your fork, you will first need to add the main repository as a remote to your repo:
git remote add upstream https://github.com/BrainNetworksCourse/brain-networks-course.git
After doing this once, you can then use the following command within the repo directory to pull the latest changes:
git pull upstream master
You may need to commit any changes you have made to other files in your repo, or use git checkout <filename> to pull a clean version if you don’t need to keep the changes.
Once you have done this it should pull down the new Vagrantfile, and you can then run vagrant provision in the main repo directory which will rerun the provisioning and install any new software.