Wednesday, October 10, 2012

FSL 5.0 Released

I don't know how I missed this, but last month a major version of FSL was released: 5.0. This means that:
  1. Everything I had previously written about FSL is now obsolete, and you were a fool to read it; and
  2. There have also been changes to processing anatomical datasets, field maps, and independent component analysis, which look interesting. Interesting, as in, I don't completely understand all the changes they made, but they look impressive.
I haven't had much time to sink my paws into it, but it looks similar to FSL 4.x. More details to come.


  1. hi! Andy, I am trying to learn FSL.
    But, unfortunately, I failed in the installation step.
    when i type in "fsl" in the terminal. it shows the following error message.
    bash: /usr/local/fsl/etc/fsl/ No such file or directory
    Could you please tell me how to solve the problem?

    1. Hey there,

      It could be because you don't have the path set correctly. Make sure that you ran the; also check your Unix source script to make sure you have something like the following code in there:

      #Set up FSL Path
      setenv FSLDIR /usr/local/fsl
      source ${FSLDIR}/etc/fslconf/fsl.csh
      setenv PATH ${FSLDIR}/bin:${PATH}

      Note that I am using the T-shell here; for bash, you would want something like this:

      . ${FSLDIR}/etc/fslconf/
      export FSLDIR PATH

      Check this link for more help:



  2. Hello,
    I am using linux and very beginner. I have edited .bashrc file in hidden home files. However, when I write directly fsl to terminal I am having an error as:couldn't connect to display "localhost:0.0"
    Error in startup script: couldn't connect to display "localhost:0.0"
    while executing
    "load /usr/local/fsl/extras/lib/ Tk"
    ("package ifneeded" script)
    invoked from within
    "package require Tk"
    invoked from within
    "if { [ string match -nocase *wish* $MYSHELL ] } {
    package require Tk
    # tk_focusFollowsMouse
    #bind Button { focus %W ; tk::ButtonEnter ..."
    (file "/usr/local/fsl/tcl/fslstart.tcl" line 18)
    invoked from within
    "source [ file dirname [ info script ] ]/fslstart.tcl"
    (file "/usr/local/fsl/tcl/fsl.tcl" line 71)
    invoked from within
    "source ${FSLDIR}/tcl/${origname}.tcl"
    (file "/usr/local/fsl/bin/fsl" line 22)
    Any suggestions how to solve this error?
    Many thanks