Choose an Access Method
The mindhive servers are in a locked closet in a cooled room, so people don't just sit in front of them and type away; they log into them remotely. There are several ways to do this.
One popular way to log into a remote Linux server is via SSH, which is short for S
ell. SSH looks like an old-fashioned text console, maybe a bit like the one David Lightman used in Wargames.
You run an SSH Client on your computer - whether your computer runs Mac OS, Microsoft Windows, some flavor of Linux, GNU/Hurd, iOS, or SkyNet. This is usually a fairly nondescript piece of software. Most operating systems except Microsoft Windows have this program built-in. If you use Windows, you can download the MIT standard software suite, SecureCRT and SecureFX from the IST Software Distribution site at http://ist.mit.edu/services/software/securecrtfx/6x .
SSH is purely text-based, so it is used for running commands that don't require fancy graphics, e.g., visualization software like Freesurfer. It is, however, pretty good for doing things like moving files around, running programs that don't need a GUI (like bedpostx or recon-all), or checking out the load on a server.
If you are running MacOS or Linux, running SSH is pretty easy. Just open up a command terminal, and type the following:
... where "username" is, of course, your own username, and the N is the number of one of the servers. Currently, these are the available servers for login:
Great, But I Use Windows.
Doh! Well, running ssh is a little more painful on Windows, but can be done. As previously noted, you'll need to download and install the SecureCRT/SecureFX from IST. Once that is done, you can launch SecureCRT, and enter the hostname of the server to which you'd like to connect, your username, and your password. If enough people have trouble using SecureCRT, I'll add a HOWTO here...
And Now What?
Once you are logged in, a bunch of default settings will get initialized for you, depending on which lab you said you were working for primarily when you requested your account. This is all controlled through a facility called dot-mindhive. You can read more about this in the "Customizing your login files" page of this manual.
You can run any of the thousands of Linux commands available to you from your new shell, but this is outside the scope of this manual. Chances are, though, at some point you are going to want to run graphical programs like Matlab, SPM, Freesurfer, AFNI, and so forth. The next section explains how to get a graphical desktop session running.