|
Size: 1961
Comment:
|
Size: 1525
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 11: | Line 11: |
| On our system, the current version of FSL (that is, the version you get by typing 'fsl' at the command prompt) is the one pointed to by the link `/imaging/local/linux/fsl`. At the time of writing this is the slightly outdated 3.2 version. |
|
| Line 17: | Line 15: |
| Any problems, report them to MatthewBrett or RhodriCusack. | Any problems, report them to RhodriCusack. == Using the latest version of FSL == Before running any other fsl command you need to run {{{ fsl_4.1.0_setup }}} which is the latest version of fsl at the moment. By running this command you also have load sharing with any fsl commands. |
| Line 31: | Line 39: |
You can check which version of FSL you are getting by typing `fsl` at the unix prompt, and looking at the version number at the top of the FSL button window - for FSL 3.3.11 it should read FSL 3.3. Oddly, you can't check which version of FSL you are getting by typing `which fsl` in unix - because, the version that you actually get depends on the `FSLDIR` environment variable, which can be mis-set, without the fixes above. |
FSL information
FSL is the FMRIB Software Library. It is a C / C++ / Tcl/Tk package written by the Oxford analysis group.
For more information see:
Main page: http://www.fmrib.ox.ac.uk/fsl
FSL course notes: http://www.fmrib.ox.ac.uk/fslcourse/
You can find the FSL example data set (http://www.fmrib.ox.ac.uk/fsl/feeds/doc/index.html) in /imaging/local/fsl/feeds.
The data for the FSL course is in /imaging/local/fsl/fslcourse.
Any problems, report them to RhodriCusack.
Using the latest version of FSL
Before running any other fsl command you need to run
fsl_4.1.0_setup
which is the latest version of fsl at the moment. By running this command you also have load sharing with any fsl commands.
Using a specific version of FSL on the CBU systems
If you need to use a specific version, rather than the one pointed to by /imaging/local/linux/bin/fsl, then define the path to the version of FSL you want, and put something like this at the end of your ~/.cshrc file:
# FSL stuff
setenv FSLDIR /imaging/local/linux/bin/fsl-3.3.11
source ${FSLDIR}/etc/fslconf/fsl.csh
set path = (${FSLDIR}/bin $path)In order for this to work when you login across linux machines, you will (I'm afraid) also need to put the same lines in your ~/.login file. Put these lines somewhere between the lines # Space for personal defaults and # End space for personal defaults in the ~/.login file.