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Brain picture
Beauchamp Lab Notebook

Updating AFNI

AFNI is frequently updated, so it is important to make sure you have the most recent version. Here is an easy way to update (for Intel Macs):

 set pkg = macosx_10.4_Intel
 tar xvfz {$pkg}.tgz

Optionally, it can be good to test the new version BEFORE overwriting the old version. Here is how we can test SUMA:

 cd macosx_10.4_Intel

If it works, we copy it over the old version (type "which afni" if you are not sure which directory afni is in)

 mv macosx_10.4_Intel/* /Applications/AFNI/
 rm -r macosx_10.4_Intel  macosx_10.4_Intel.tgz

X11 and XTools

X11 is the display system for Macs and most Unix machines. XTools is a programming environment for the Mac that includes useful compilers and other software tools. To install X11 and XTools on the Intel Macs find the Install Discs that came with your Mac, go into the System Installation Packages folder, and install the relevant pkg files. After installing X11, it will be useful to switch the default shell to T-shell. Type the following into an X11 window:

chsh –s /bin/tcsh

The T-shell is particularly convenient because it can retrieve previous lines entered with the up arrow key and it can also automatically complete file names with the tab key. Note that this command requires you to quit and restart X11 for changes to take effect.


Fink is a program package manager for Macs. Download the program from the Fink webpage:

The program in the dmg file will be straightforward. You can copy finkcommander to the applications folder for a GUI interface. You should update your libraries every few weeks by running the following: fink selfupdate; fink update-all

Installing Required Libraries for AFNI

Type the following line to have Fink grab the newest versions:

fink install glib2-dev glib netpbm openmotif3


AFNI is a suite of programs developed at the NIH for the analysis of functional neuroimaging. The best place to go for installation directions is AFNI’s instruction website:

Unlike the NIH, we install AFNI to the /Applications/abin folder, rather than the local folder of each user. If you want the most up to date version, click the link for compiling AFNI under Mac OS X. You should also check the download webpage each month for updates:

To include AFNI in the path, paste the following line into a terminal window:

echo 'set path = ( $path  /Applications/abin )' >> ~/.cshrc


FreeSurfer is another set of programs developed at NIH for the analysis of functional neuroimaging. We mainly use it for cortical surface reconstruction. Their download page is part of an extensive wiki that describes its many functions.

Updates to the software are normally posted on the listserv. To set the correct paths for Freesurfer paste the following lines into a terminal window:

echo ‘setenv FREESURFER_HOME /Applications/freesurfer‘ >> ~/.cshrc
echo ‘source $FREESURFER_HOME/SetUpFreeSurfer.csh' >> ~/.cshrc


Go to Caret's Download Webpage, register for an account, and download the newest release. Copy the caret folder to the Applications folder on your machine and add the following line to your .cshrc file:

  set path = ($path /Applications/caret/bin/)

Creating Symbolic Links

It is useful to have symbolic links from the command line so you do not need to type the full path to a file. The program ln creates such symbolic links. Here are a couple of examples:

ln –s /Volumes/data9/surfaces/ /surfaces
ln –s /Volumes/data1/UT /UT

The paths are now linked to /surfaces/ and /UT/.

Installing the Dell Printer Drivers

The application Dell 5100cn Installer is on data9. The printer IP is To see the current status of the printer go to

Here is a copy of the manual

Mounting RAID Volumes from Windows

You must have a Mac with a valid user account. On the Mac, go to System Preferences, Sharing, and enable Windows Sharing. The menu should say

 Windows users can access your computer at \\XXX.XXX.XXX.XXX\YYY

You may also need to able your user account. Look for the message

 Enabled accounts: Ashley Kingon

If your account is not enabled, click on the "Accounts" button and enable it.

In Windows, go to Network and add this connection.

Mounting a Volume after sshing to a different machine

For example. I ssh onto tellmore machine. Now I want to access data9 from his machine.

in my home directory (~) (on tellmore) I make a directory called mount, inside of mount I make a directory called data9 (or which ever volume I am mounting), then I mount data9.

cd ~
mkdir mount
cd mount
mkdir data9
mount_afp -i afp://akingon@ data9
enter password 

and now you can cd into data9

Installing Matlab

To install Matlab for use in the Beauchamp lab:

1. Download and install matlab here. Get login name and pw from Mike
Note: you will be prompted to install Java run-time environment 5. This will ease the installation.
2. Place license.dat in the MATLAB folder when prompted.
3. Find out that Matlab is already on the computer and cancel installation.

Lab Printer

The lab laser printer is a Dell 5100cn with IP address You can check the printer status by going to In Windows, you must add a Port with this address, then install the correct printer driver and tell it to print to the port. On the Mac, go to System Preferences, Print & Fax, Click the +, Click IP, enter the IP into the address field.