Downloading
FSL is available as a single package. As well as the FSL source
distribution, which needs compiling before it can be used, FSL is
available precompiled (including all necessary third-party software)
for some platforms. If you want to just run certain tools then the
easiest thing to do is take the appropriate precompiled distribution
and find the relevant program in fsl/bin.
Download
FSL
Unpacking
To unpack a distribution, you need gunzip and tar. Type
gunzip ???whatever???.tar.gz
tar xvf ???whatever???.tar
Compiling the source distribution
If you have not taken a precompiled version, you will require:
- GNU make
(this should be named gmake to make sure that FSL uses this rather
than any other "make" in your path)
- GNU
install (this should be named ginstall to make sure that FSL
uses this rather than any other "install" in your path)
- GCC C/C++
compiler (gcc-2.95.2, gcc-2.95.3 and gcc-2.96 seem to work ok;
gcc-3 is not yet supported)
- convert and display from the ImageMagick package with
added TIFF support (place convert and display in fsl/bin)
- gnuplot (place
gnuplot in fsl/bin)
- Tcl and Tk and
Tix (configure all three
with configure --prefix=$FSLDIR before installing and compile
Tix with make CC='cc -fwritable-strings').
Then cd into the top level (fsl) and type BUILD.
Running
First, set environment variable FSLDIR to the top fsl directory name,
e.g. /usr/local/fsl . Next, include ${FSLDIR}/bin in your path.
To run the FSL tools from the command line, you can find the tools
in fsl/bin. Where there is a choice between GUI and non-GUI version of
a tool, the non-GUI version is fully lower case (e.g. 'bet'), whilst
the GUI version is capitalised (e.g. 'Bet'). "fsl" is a simple GUI
which will start up the main individual FSL GUI tools - you probably
want to start with this.
All programs use Analyze (AVW) format files, as used by Analyze,
MEDx, SPM etc.
Some of the tools are separately compiled for each
image data type (8-bit unsigned, 16-bit signed, etc.) named e.g.,
bet_8UI, bet_16SI, etc. Note that there is a mechanism in place to
choose which to call automatically; e.g., bet detects which data type
is being processed, and then calls the appropriate binary name on the
basis of the original program name (e.g. bet) and the data type
(e.g. 16SI).
Quick start
(If you don't know what shell you are using, try both of the following)
bash users: export FSLDIR=/usr/local/fsl; export
PATH=$PATH:$FSLDIR/bin; $FSLDIR/bin/fsl
tcsh users: setenv FSLDIR /usr/local/fsl; setenv PATH
${PATH}:$FSLDIR/bin; rehash; $FSLDIR/bin/fsl
Running FSL on Apple Mac
The binary distribution of FSL for Apple Mac requires Mac OS X (tested
under 10.1 and 10.2). If you are happy to run FSL tools from the
command line, then you need install NO other software on your Mac
(simply set FSLDIR to the top fsl directory name as described above
and include ${FSLDIR}/bin in your path). If you want to use the FSL
GUIs then you will need to install X windows on top of Mac OS X (by
default Mac OS X comes with a different window system - Aqua - which
can work alongside X but which cannot on its own run X windows
programs such as the FSL GUIs).
Installing X on Mac OS X is easy:
- Go to Fink ->
Documentation -> Running X11 -> Getting and Installing XFree86.
- For the simplest installation you only need the XFree86 official
binaries (we used 4.1.0/binaries/Darwin-ppc - download all files
in there and then run "sudo sh Xinstall.sh" in a terminal on your Mac).
Windows program for viewing AVW images
There is a nice tool (separate from FSL), for viewing AVW images
(including colour AVW images generated by FSL) - go to 3D
VisionWorks.