Beauchamp:Software Installation
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Beauchamp Lab Notebook
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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 wget http://afni.nimh.nih.gov/pub/dist/tgz/{$pkg}.tgz tar xvfz {$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 ./suma
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 a couple of useful compilers. Right now Apple does not provide these programs for the Intel Macs on their website. To install X11 and XTools on the Intel Macs find the Install Disc 1, go into the System Installation Packages folder, and install the useful 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
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
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:
http://afni.nimh.nih.gov/pub/dist/HOWTO//howto/ht00_inst/html/index.shtml
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:
http://afni.nimh.nih.gov/pub/dist/tgz/
To include AFNI in the path, paste the following line into a terminal window:
echo 'set path = ( $path /Applications/abin )' >> ~/.cshrc
FreeSurfer
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.
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
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 $FREESURFER_HOME/SetUpFreeSurfer.csh' >> ~/.cshrc
Caret
Go to Caret's Download Webpage, register for an account, and download the newest release. Copy the caret folder to the Applications folder on your machine and add the following line to your .cshrc file:
set path = ($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 129.106.236.253 To see the current status of the printer go to http://129.106.236.253
Here is a copy of the manual http://openwetware.org/images/8/83/Dell_5100cn.pdf
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@129.106.236.180/data9 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 139.52.6.205 You can check the printer status by going to http://139.52.6.205 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.
Magstim Rapid TMS
This is our TMS (Transcranial Magnetic Stimulation) machine from Magstim company, UK. The front panel controls are:
- 1.Standby
- 2.Run (arm, bring out of standby)
- 3.Stimulus intensity control
- 4.Trigger
Alternatively to trigger the device, a TTL pulse can be sent to the "Trigger In" port in the back of the device with a BNC connector.
The machine can also be controlled externally via the 36pin Centronics connector in the back panel. A Parallel printer cable can be used/made with a DB25 male connector on one end to connect to PC Parallel Port and a Centronics 36pin male connector on the other end to connect to Magstim Rapid.
NOTE: ECP/EPP needs to be selected for the Parallel Port in BIOS.
A 5V input should be connected to Pin 1 of the Centronics connector to gain external control (either from an external source or by downstepping the available 12V at pin 15 of the Centronics connector.
A 7 bit binary code through pins 2-8 can set the stimulus intensity (only values between 10 and 100 can be used)
Pin 9 is used for triggering by applying a 0.
Magstim catalog mentions not to use the BNC trigger input when using this trigger instead.
