Updating FreeSurfer and FSL

Updates (or "patches") are available from the FSL and FreeSurfer websites, and can be installed with a few manual steps.

FSL

The current version is displayed at the top of the FSL GUI (see below). It is also shown in the help, for example version 5.04:

[user@localhost ~]$ randomise --help 
 
Part of FSL (build 504) 
randomise v2.9 

...

Go to the FSL patch download location (http://fsl.fmrib.ox.ac.uk/fsldownloads/patches/). (See right for more details.)

Select the correct file; this is tricky because the files look the same unless the cursor is over it, when you can read the name in the status bar. Look for the Linux version (Centos 6 64-bit ), and the file that starts from the current version; if not sure choose the one that includes all patches (with the "x" in it, e.g., 5.0.x below); this will usually be larger. The other file only upgrades the latest step (the size will be smaller).

Download this file, and move it to the LinuxShare folder.

In Linux, copy this file to the folder "/usr/local" (Use the FIle Browser):

Open a terminal in /usr/local

• Either open a terminal as per usual and go [user@localhost temp]$ cd /usr/local, or from the File Browser (see right).

Make sure FSL is not running

Running the following command to unpack the new files and overwrite the old version; the filename will change.

[user@localhost temp]$ tar -zxvf fsl-centos6_64-patch-5.0.9_from_5.0.x.tar.gz

Note: once you start typing the file name, use the Linux feature where "Tab" brings up the remainder of the file name.

You will see a list of files copied from the "tar ball"; the upgrade is complete once this command is finished. You can check the version by running the fsl GUI:

[user@localhost temp]$ fsl

You can delete all the tar.gz files, including any in usr/local, LinuxShare, or Windows.