FSL

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[edit] FSL via Linux Command Line (VISTA LAB INTERNAL)

Various versions of FSL are installed on a remote machine (white) and you can run FSL tools via the command line within an xterm. In order to do this you must edit your .bashrc file. If you're on a windows or mac machine (esp. laptop) you can download and install FSL using the links below.

[edit] Editing the .bashrc file

  • The .bashrc file can be found in your home directory on white:
 /user/YourUserName/.bashrc (use ls -a to list the .bashrc file, which is a hidden file).
  • Edit the .bashrc file by pasting the following lines of code at the end of the file:
   export FSLDIR=/usr/local/fsl/v4.1.9/
   . $FSLDIR/etc/fslconf/fsl.sh
   export PATH=$FSLDIR/bin:$PATH;

Note: You can edit the .bashrc file, or any text file, by typing nano .bashrc at the unix prompt. This will allow you to edit the text file right in the command line. If you want to edit the file with a GUI you can use MATLAB's Editor or just open the file via windows explorer with a text editor.

[edit] Running FSL Tools

  • Now, to get the FSL menu to pop-up when you type fsl at the command prompt you must log in using -Y after the ssh command. If you don't you will get a DISPLAY error message. If you do just exit and log in as in the example below.
 ssh -Y -X username@teal.stanford.edu

[edit] Download and Intallation

[edit] FSL on Linux Platforms

Please see the FMRIB website for excellent installation instructions.

[edit] FSL on Windows Platforms

Please see the FMRIB website for excellent installation instructions.

[edit] FSL on Mac Platforms

Please see the FMRIB website for excellent installation instructions.

[edit] FSL Tools

For information regarding the FSL tools please visit the FSL site.

[edit] Libraries (Fedora Linux)

You will need to install expat for FSL to work properly... To do this in Fedora:

 sudo yum install  expat-devel compat-expat1
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