FSL

Compiling 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 (versions from gcc-2.95.2 to gcc-3.4 seem to work fine in general, though gcc-3.3 upwards on Cygwin doesn't work - we used gcc-3.2 for our current Cygwin release).
In addition, the following are required:
(Note: sometimes these binaries can be taken from one of the other FSL binary distributions if the operating system and machines are similar - e.g. certain varieties of linux on PC machines)
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 version 8.4.7.0 and Tix version 8.1.4 (configure all three with configure --prefix=$FSLDIR before making and installing).

Then do the following check (this if for the bash shell; if you are using tcsh amend appropriately):

Set the main FSL environment variable:

export FSLDIR=<??wherever fsl is unpacked??>
e.g. export FSLDIR=/usr/local/fsl

Then source the FSL environment setup script:
```
. ${FSLDIR}/etc/fslconf/fsl.sh
```
Then check if your machine/compiler is supported by default:
```
ls $FSLDIR/config/$FSLMACHTYPE
```

If the above directory does not exist (the ls returns an error):

Select the closest match from the directories in $FSLDIR/config and do the following:
```
cp -r $FSLDIR/config/closestmatch $FSLDIR/config/$FSLMACHTYPE
```
Depending on how different your machine and compiler are from the closest match, you may need to edit the files inside the $FSLDIR/config/$FSLMACHTYPE directory which set the local paths and variables for things like install commands, compiler flags, etc.

Once this test is done then the sources can be built simply by doing:

cd $FSLDIR
./build

If you want to re-make a particular package in $FSLDIR/src (e.g. flirt) then first set the FSLDEVDIR environment variable to the same as FSLDIR and then just type make install inside the relevant directory.