Dear All,

 

With the help of the people at freesurfer I managed to get freesurfer working on the newly available distribution of Fedora Core 2. This mail covers an account of how we managed to get things working, so it is less informative to people who are not planning to use Fedora Core 2.

 

My system hardware:

CPU: Dual Intel Xeon 2.4 Ghz (HT disabled)

Video: Nvidia Geforce 4 TI 4600

RAM: 2 GB

 

Required Software:

Fedora core 2 -> can be downloaded here http://fedora.redhat.com/download/mirrors.html

Fedora kernel compiled with 8 stacks -> http://www.linuxant.com/driverloader/wlan/full/downloads-fc2-kernel-i686.php

Nvidia Linux driver v53.16 -> http://www.nvidia.com/object/linux.html

Freesurfer -> version of February 18th 2004 http://surfer.nmr.mgh.harvard.edu/download.html

TCL/TK 8.3.5 -> sources http://www.tcl.tk/software/tcltk/downloadnow83.html

 

 

Overview of the installation:

Step 0: Download all the required packages

Step 1: Install Fedora

Step 2: Install Fedora kernel compiled with 8 stacks (required for compatibility with the Nvidia driver)

Step 3: Install Nvidia driver

Step 4: Install Freesurfer

Step 5: Compile and install TCL/TK

Step 6: Let’s play with Freesurfer

 

Installation details:

 

Step 0:

Make sure to have all the packages before starting the installation. If you already have Fedora Core running on your system, download the remaining packages and start at Step 2.

 

Step 1:

Installation instructions for downloading and installing Fedora Core 2 are covered on the fedora project website. (www.fedora.redhat.com).

Make sure to use the tc or c shell. You can set your default shell in /etc/passwd. Fedora Core 2 runs bash by default.

 

Step 2:

Download the kernel compiled with 8 stacks or compile it yourself. Both the normal and smp (multi processor) core are available from the website above. Installation of the rpm is simple. First unzip and then

 

rpm –i kernel-smp-2.6.6-1.427.8kstacks.i686.rpm

 

Next, reboot into the 8kstacks kernel and start with runlevel 3. You can set the default runlevel in /etc/inittab.

 

Step 3:

Installation of the Nvidia driver can only be performed from the command line. The X server should not be running. Installation instructions for downloading and installing the driver can be found here ftp://download.nvidia.com/XFree86/Linux-x86/1.0-5336/README.

 

Once installed, check to see if your OPENGL GLX driver is working properly. Type at the command line:

 

glxinfo

 

Check that direct rendering is set to YES

 

Next, type

 

glxgears

 

Can you see the gears rotating? How many frames do you get?

 

If this is all working, you are ready for the next step.

 

Step 4:

Install Freesurfer. Installation instructions for downloading and installing Freesurfer can be found here ftp://surfer.nmr.mgh.harvard.edu/pub/docs/INSTALL. Make sure to correctly setup the shell and all variables, as is outlined in the installation documentation. To check if tkmedit and tksurfer will make proper use of the nvidia driver, type

 

ldd /usr/local/bin/freesurfer/bin/Linux/tkmedit

 

and also

 

ldd /usr/local/bin/freesurfer/bin/Linux/tksurfer

 

Note the files being used for libGL and libGLcore -- if they are something other than the NVIDIA libraries, then you will need to either remove the libraries that are getting in the way, or adjust your ld search path.  (See the Nvidia driver installation manual.)

 

Step 5:

Fedora Core 2 comes with the latest release of TCL/TK (=8.4.X). Since tkmedit and tk surfer are compiled with the 8.3.X version, an incompatibility exists and tkmedit and tksurfer will not start properly. In order to overcome this problem you will have to compile TCL/TK 8.3.X for your system and point tkmedit and tksurfer to the right version. You can learn how to do this here http://www.tcl.tk/doc/howto/compile.html. Since there are no 8.3.X binaries compiled for Fedora Core 2, I see no other option than compiling your own. This is relatively simple by typing the commands below in the /usr/src/tcl8.3.5/unix source path (or wherever you unpacked them). The same goes for tk8.3.X

 

./configure

make

make test

make install

 

Finally I created a symlink in /lib pointing to /usr/lib/tcl8.3.x by typing

 

ln –s –i /usr/lib/tcl8.3.x/libtcl8.3.so.0  /lib/ libtcl8.3.so.0

 

and the same for tk

 

ln –s –I /usr/lib/tk8.3.x/libtk8.3.so.0  /lib/libtk8.3.so.0

 

Step 6:

Happy playing.

 

 

drs. Niels M. van Strien

Vrije Universiteit Medisch Centrum
Department of Anatomy, room MF-G102 b

Van der Boechorststraat 7
P.O. Box 7057

1007  MB  Amsterdam
The Netherlands

 

e-mail: n.vanstrien@vumc.nl

phone: +31 (20) 4448047

fax: +31 (20)