Verify your installation

Verify your installation

To check that FSL has been installed, close and re-open your shell/terminal, and then follow the steps below. If any of the steps don't work, check the troubleshooting page for some potential solutions.

1. Type echo $FSLDIR into the terminal, and press enter. This should print out the location that FSL has been installed to, e.g. /Users/steve/fsl/.

2. Type fslmaths into the terminal, and press enter. You should be presented with the help text for the fslmaths command:

   $ fslmaths
   
   Usage: fslmaths [-dt <datatype>] <first_input> [operations and inputs] <output> [-odt <datatype>]
   
   Datatype information:
    -dt sets the datatype used internally for calculations (default float for all except double images)
    -odt sets the output datatype ( default is float )
    Possible datatypes are: char short int float double input
    "input" will set the datatype to that of the original image
   
   ...
   

3. Type imcp into the terminal, and press enter. You should be presented with the help text for the imcp command:

   $ imcp
   
   Usage:
     imcp <file1> <file2>
     imcp <file1> <directory>
     imcp <file1> <file2> ... <fileN> <directory>
   
   Copy images from <file1> to <file2>, or copy all <file>s to <directory>
   
   NB: filenames can be basenames or include an extension.
   
   Recognised file extensions: .nii.gz, .nii, .img, .hdr, .img.gz, .hdr.gz
   

4. Type fsl & into the terminal, and press enter. The FSL GUI should appear:

1. Type fsleyes -std & into the terminal, and press enter. The FSLeyes image viewer should start up, and display the MNI152 T1 standard template:

If all of the above steps work, you have successfully installed FSL. If any of the steps do not work, refer to the troubleshooting page for some suggestions.