FslMaintenance - MRC CBU Imaging Wiki

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FSL Maintenance Info

This is for maintaing FSL software on the CBU cluster.

FSL Path Structure

All FSL software lives in: 

/imaging/local/software/fsl/
/imaging/local/software/fsl/fsl64/
/imaging/local/software/fsl/fsl64/fsl-4.1.2/
/imaging/local/software/fsl/fsl64/fsl-4.1.4/
...
/imaging/local/software/fsl/fsl32/
/imaging/local/software/fsl/fsl32/fsl-4.1.2/
/imaging/local/software/fsl/fsl32/fsl-4.1.4/
...

NOTE: the /software/ folder is NOT added to people's path. Hence, all scripts to run FSL are placed in a different folder, which is added to users' paths: 

/imaging/local/scripts/

Installing a new FSL version

(The detailed instructions are available on the FSL website: http://www.fmrib.ox.ac.uk/fsl/fsl/downloading.html )

When a new version comes out do the following:

  1. Create a new folder (e.g. /imaging/local/software/fsl/fsl64/fsl-#.#.#/)
  2. Download in there the new version file (typically a .tar.gz file)
  3. unzip/untar in that folder (e.g. tar zxvf fsl-*-centos5-64.tar.gz).

As a result, the actual commands for the new version should now be found in the following path (for, say, version fsl-5.0.1 64bit) 

/imaging/local/software/fsl/fsl64/fsl-5.0.1/fsl/bin/

(NOTE: make sure everything is owned by the imagers_devel group: e.g. chgrp -R imagers_devel /imaging/local/software/fsl)

Testing New FSL Versions

FSL has a little tool called FEEDS suite that can be used to run tests on a new FSL installation, to check that all the bits and pieces run smoothly. I [MM] created a small script that allows to run the FEEDS suite on whichever version you want (I show the help line that is printed if you omit the two arguments): 

> ./Run_Feeds_Evaluation.csh

*****USAGE: Run_Feeds_Evaluation.csh 'fslver' 'fslbit'
'fslver' is the FSL version (e.g. fsl-4.1.4)
'fslbit' is the 'bit' version (i.e. 64 or 32) [default 64]

The only presupposition of this script is that the version you want to test (fsl-#.#.#) has been unpacked in the following path:

/imaging/local/software/fsl/fsl64/fsl-#.#.#/fsl (for the 64 bit)

/imaging/local/software/fsl/fsl32/fsl-#.#.#/fsl (for the 32 bit)

EXAMPLES:

To test the latest fsl (4.1.4 64bit) you just have to type: 

./Run_Feeds_Evaluation.csh fsl-4.1.4

(The script will warn you that if the second argument is missing it defaults to 64bit)

To test the 32bit version, however, you have to specify that: 

./Run_Feeds_Evaluation.csh fsl-4.1.4 32

Once you launch the command it will ask you to check the FSL path and version details before running FEEDS. Once testing is done, the info is saved by default in a file named Feeds_Report_fsl-#.#.#_##bit.log. The important thing is that no error exceeds 1% (in fact the last line of the log should let you know whether all errors are below 1%). If you get errors in excess of that figure and you are sure the installation was correct, you may want to send the log to the FSL people for help.

See the FEEDS page here: http://www.fmrib.ox.ac.uk/fsl/feeds/doc/index.html