In order to use the computers at the link, you must have access to the AFS (Andrew File System) space and Webfiles (webfiles.duke.edu). Having a NetID is necessary but not sufficient; you must also have a Webfiles account and you can request one from OIT if you don't already have one. If you're enrolled in the class, you should already have one. Only auditors should lack this account at first.
To log into the computers, you have to use your NetID and password. Once you log on, you will automatically be able access all class-related files, which will be accessible by double clicking on the datasets or classwork symlinks on the desktop. These symlinks will take you to /afs/acpub/projects/neurobio381/[datasets or classwork] depending on which one you click on. You will have read-write access to classwork and read-only access to datasets.
To get to the applications, you must first click on the Finder in the lower lefthand side of the screen. After that, you then click “Go” and then “Applications”. Once you have a window open with all the applications, find the one you want and simply double-click on it. The only exception to this is FSL, which must be opened through the terminal window.
The first time you use Office, you may have to go through a short registration process where it may ask you to download updates. Don't worry about the updates – odds are you won't be able to do them anyway since you are not admins.
This application will be in a folder (MATLAB7.6 ?) in the Applications folder. Once you open MATLAB, many paths will already be set up; however, you will often have to add the path to the Scripts directory inside of Examples for many of your MATLAB labs.
This application will allow to you create cool images that can be used in your presentations/papers. It is located inside the applications folder, and it is really easy to use.
Accessing FSL is a bit different from the other applications you will use in the fMRI class. You open it via the command line in the terminal. So, to open the terminal you need to go to the Utilities folder instead of the Applications folder. From there, you'll want to double-click on the application called “Terminal”. Once you have the terminal open, I suggest navigating to the class space before open FSL. To do this, simply type
cd /afs/acpub/projects/neurobio381. This will save you some unnecessary browsing when you're trying to find files in FSL.
Now to open FSL, type
fsl & and hit return. The ampersand (&) at the end backgrounds the process and allows you to still type commands in the terminal if you need to. If you forget it, you won't be able to enter commands until you terminate the process.
Recall that you only have read-write access to the classwork folder, so obviously you won't be able to conduct analyses anywhere except within classwork.