What To Do

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How to setup your computers.

aclark

Details of classroom setup. Largely based on the experiences of the SSCC in AFNI Bootcamp.

Page 2 of 3.

If you have made it this far then you probably have a date, a time, a classroom, some students, and one or more teachers to teach AFNI. Now you need to setup your computers. Here are the steps.

1. Create User

The first thing to do is create a generic user account on your system preferably with a password that is easy to type. You don't want to spend 15 minutes walking around the class and helping people type "4FN1isC00L" just to get started. You also don't want to walk around and login to every workstation. We write the password in huge letters on the classroom whiteboard.
Unfortunately adding users is beyond the scope of this document. If you aren't familiar with the process, contact a system administrator or unix geek in your group. I will only give a brief overview here:

We create a normal user called "user" with the password "afni123" and no administrative privileges.

In Linux, the commands (run as super-user) look like this:

[root@foo ~]# adduser user
[root@foo ~]# passwd user
Changing password for user user.
New UNIX password:
Retype new UNIX password:
passwd: all authentication tokens updated successfully.

There are also graphical programs to administrate users in Linux.

In Mac OS X:

Click on: Finder -> System Preferences -> Accounts -> Click the lock to make changes -> +

Enter these fields:

Name: user

Short Name: user

Password: afni123

Confirm: afni123

Click on: Finder -> System Preferences -> Quit System Preferences.

2. Change Shell

Once you have created a user you should change the user's shell to "tcsh". Again, that is beyond the scope of this document, but here is an overview:

In Linux, one way would be to run the "chsh" program.

This has the advantage of being simple, but the disadvantage of using the default editor "vi", which may confuse some people.
A possible solution is to set the EDITOR environment variable to another user friendly editor like nedit then run "chsh", shown in Mac OS X here but the idea is the same:

In Linux, another way would be to edit the /etc/passwd file with your favorite text editor.

Find the line with your user on it and change "/bin/bash" to "/bin/tcsh".

It will look something like this before:

user:x:517:518::/home/user:/bin/bash

and this after:

user:x:517:518::/home/user:/bin/tcsh

In Mac OS X:

Click On: Finder -> Applications -> Utilities -> Netinfo Manager -> users -> user -> Click the lock to make changes -> shell ->

Edit the "shell" field

Change "/bin/bash" to "/bin/tcsh"

You can also use the "chsh" program to change your shell in Mac OS X (as shown above).

3. Install Binaries

There are many ways to accomplish this, the process is explained in detail in‚ HowTo #00.
For now I'll explain the simplest case:

Go to the website and download a binary distribution.

Navigate to http://afni.nimh.nih.gov/afni/download/afni/releases/latest and choose the appropriate binaries for your hardware/operating system. (How do you pick the appropriate binaries? That can be confusing. If you aren't sure which ones to pick, post a question to the message board.)

Extract the contents to the user's home directory.

At this point you should have a linux_gcc32.tgz or macosx_10.3.tgz file downloaded.
In most unices you can type:


tar -zxvf linux_gcc32.tgz

mv linux_gcc32 abin

4. Install Sample Data

Essentially you want to download the Sample Data files and extract them in the user's home dir. In addition we have some scripts that may help you with this process.

First the data. You will need:

AFNI_data1.tgz

AFNI_data2.tgz

SUMA_demo.tgz

SUMA_StandardMeshes.tgz

dicom.tgz

Second, installing the data.

In most unices you should be able to do:

Get rid of the old data (in case you already taught class on the same computer):

rm -rf AFNI_data1
rm -rf AFNI_data2
rm -rf suma_demo
rm -rf std_meshes
rm -rf dicom

Install latest data:

tar -zxvf AFNI_data1.tgz
tar -zxvf AFNI_data2.tgz
tar -zxvf SUMA_demo.tgz
tar -zxvf SUMA_StandardMeshses.tgz
tar -zxvf dicom.tgz

5. Install Dot Files

These are the hidden system files that allow you to customize your environment to run AFNI. They should go in the user's home directory.

6. Optionally use the AFNI Bootcamp CD

In order to streamline the above process you can use our install CD to automate steps 4 & 5.
Unfortunately the process of burning a CD is beyond the scope of this document, but here is an overview:

In a subdirectory of the data directory we keep a CD directory that contains all of the data and dotfiles mentioned above, as well as three shell scripts to automate the installation process. There is also a compressed archive of the CD directory located in the data directory.

Assuming you have transferred the contents of the CD directory or CD.tgz to a CDROM, then do the following:

login as your afni user
mount the cdrom (sometimes done for you automatically by autofs in linux)
mount /mnt/cdrom
run s1.rm.old.data ~
run s2.cp.data /mnt/cdrom ~

Note: the dicom.tgz package is not included with the CD package (as it would exceed the CD size limit).

7. Configure Ownership and Permissions

It's always a good idea in UNIX (when doing things as the super-user) to make sure your user "owns" everything that he or she should own (ie. has the appropriate ownership and permission settings for his or her files).
To that end you should issue a global-set-ownership command when you are finished installing the binaries and data.
Something like: