To install FSL on a Mac you need to do the following:
Utilities
folder within the Applications
folder; by default Macs
don't generally come with this installed (you'll almost certainly need
X11 later for things other than FSL anyway.) Optional Installs
,
then click on Applications -> X11
.
Terminal
(you can find this application in
Utilities
folder inside the Applications
folder).
cd /usr/local
tar -zxvf ~/Desktop/fsl-3.3-macosx.tar.gz
fsl
in the current
directory which will contain all the required files for FSL and
FSLView. Note that you might need to add sudo
to the
start of the
tar
command if you don't automatically have the right to
create files in /usr/local
.
open /usr/local/fsl
help
bash
shell, or an error saying "command not found" or similar message, in which case you are using the tcsh
or csh
shell.
bash
shell then do the following -
cd touch .bash_profile open -a TextEdit .bash_profile
Make Plain Text
from the Format
menu if it is available (if only Make Rich Text
is there then do nothing as it is already in plain text mode)
FSLDIR=/usr/local/fsl . ${FSLDIR}/etc/fslconf/fsl.sh PATH=${FSLDIR}/bin:${PATH} export FSLDIR PATH
Note that the second line starts with a dot (i.e. full stop or period), then a space, then ${FSLDIR}/etc/fslconf/fsl.sh
- the dot and space are very important!
FSLDIR=/usr/local/fsl
and replace /usr/local/fsl
with the directory name of the place where you installed FSL.
TextEdit
If you are using the tcsh
or the csh
shell then follow the above instructions, but instead type the following in the terminal:
cd touch .cshrc open -a TextEdit .cshrcand add the following to the
.cshrc
file (as opened in TextEdit, but after selecting plain text mode - as above):
setenv FSLDIR /usr/local/fsl source ${FSLDIR}/etc/fslconf/fsl.csh setenv PATH ${FSLDIR}/bin:${PATH}then change the
/usr/local/fsl
as instructed above, and save the file.
echo $FSLDIR
This should display the name of the directory that you installed FSL in.
flirt -version
FLIRT version 5.4.2
In general, to run the FSL tools from the command line (within a
terminal) you need to enter the program name in lower case
(e.g. bet
). Typing a command on its own (without any
arguments or options) gives you a help message for that command.
A more complete test of the FSL installation can be run at this point by using the testing and evaluation suite: FEEDS. See the FSL FAQ for more information about this.
Utilities
folder inside the
Applications
folder) . All of the FSL GUIs should now
work. To run a GUI version of a program you can either type its
capitalised name with an additional '_gui' appended in the terminal
(e.g. Bet_gui
), or you can start the main FSL GUI by just
typing fsl
.