Editing STIR FAQ (section)

= Why can't I run any of the STIR executables and/or scripts? =
STIR comes as as a set of executables and scripts. For normal usage, these need to be in the ''path'' of your shell. If this isn't the case, you will see something like
<pre>
$ generate_image mygreatimage.par
-bash: generate_image: command not found
</pre>
The exact message you would see depends on your environment.

The recommended way to solve this is to install the STIR executables and scripts into a directory and then add this directory to your path. For example on Linux (or [http://cygwin.com Cygwin]) when using the handcrafted Makefiles:
<pre>
$ cd /where/ever/is/STIR
$ mkdir /where/ever/you/want/it
$ make install INSTALL_PREFIX=/where/ever/you/want/it
$ PATH=$PATH:/where/ever/you/want/it/bin
$ LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/where/ever/you/want/it/lib
$ export LD_LIBRARY_PATH
</pre>
When using '''CMake''', you normally set the installation location when running '''CMake''', but you still need
to do <code> make install</code>. And when using '''csh''' as your shell, you need to replace the last 3 lines with csh syntax
<pre>
$ set path=( $path /where/ever/you/want/it/bin )
$ setenv LD_LIBRARY_PATH $LD_LIBRARY_PATH:/where/ever/you/want/it/lib
</pre>

If you get ''permission denied' messages when creating the installation directory (or when doing the installation) it is probably because you choose a location for which you do not have write permission (such as <tt>/usr/local</tt>). Unless you want to make STIR available to all users on a machine, it is recommended to use a subdirectory of your ''home''.

You might want to make sure that STIR is always in your path. To do that, you should copy the last 3 lines into your 
startup file. Depending on your default shell, this will be a file called <tt>~/.bash_profile</tt>, <tt>~/.bashrc</tt>, <tt>~/.profile</tt> or <tt>~/.cshrc</tt> on Unix/Linux/Cygwin. On Windows you will need to set the ''Path'' environment variable via the ''System'' Control Panel.