Current Linux - normal user

detailed instructions

    Step 0: enter these commands to prepare for the installation:
	
	cd
	mkdir abin
	

	The first command, 'cd', is used just to make sure the user is in
	their home directory, before issuing further commands.

	The second command, 'mkdir abin' is used to create the directory
	which will be used to store the actual programs from the AFNI
	package.  The main reason that 'abin' (for "AFNI binaries") is
	chosen for a name is to allow the descriptions to be more generic,
	and less dependent upon which operating system is in use.


    Step 1: enter these commands to get and unpack the AFNI binary package:
	
	wget http://afni.nimh.nih.gov/pub/dist/tgz/linux_gcc32.tgz
	tar xvfz linux_gcc32.tgz
	mv linux_gcc32/* abin
	rmdir linux_gcc32
	

	The first command, 'wget http://...' is used to actually download
	the AFNI package.  The user may use their browser, pointed to
	pub/dist/tgz to find the linux_gcc32.tgz package, also.

	The second command, 'tar xvfz linux_gcc32.tgz' is used to 
	extract the contents (the programs) of the compressed package.
	The options used with this tar command are:
	    x - to extract the contents of the archive
	    v - verbose, to display files as they are extracted
	    f - file, the next argument is the tar file to expand
	    z - uncompress the file before extracting its contents
	See 'man tar' for more details.

	The third command, 'mv linux_gcc32/* abin' moves everything from
	the newly extracted linux_gcc32 directory into the abin directory.

	The final command, 'rmdir linux_gcc32' is used to remove the
	empty linux_gcc32 directory, now that its contents have been
	moved to abin.

	Note: this linux_gcc32.tgz package includes SUMA.


    Step 2: enter these commands to get and unpack some sample data:
	
	wget http://afni.nimh.nih.gov/pub/dist/edu/data/AFNI_data1.tgz
	tar xvfz AFNI_data1.tgz
	

	The first command, 'wget http://...' is used to download the
	AFNI_data1.tgz sample data package.  This package contains
	SPGR anatomy, EPI time-series data, and an 'afni' directory,
	with datasets made from that raw data.  The user may also use
	their browser to download AFNI_data1.tgz.

	The 'tar xvfz ...' command is to extract the AFNI_data1
	directory from the compressed archive.  The tar options are
	the same as in Step 1.


    Step 3: enter this command to add the directory ~/abin to your PATH:
	
	echo 'set path = ( $path ~/abin )' >> ~/.cshrc
	

	This command, 'set path = ( $path ~/abin )' could be added to
	your home .cshrc file via any text editor.  It is given here as
	an append command (with the '>>' redirection) so that it can be
	executed via copy-and-paste on the command line.

	Note two points here.  The first is that the value of the PATH
	variable is a list of directories containing programs that you
	care about.  It is valid to run programs without using this
	variable (e.g. by running '/bin/ls' or /home/pickle/abin/afni'),
	but it is less convenient (most people would rather just enter
	commands as 'ls' or 'afni').

	The second point is that in the T-shell (or C-shell), the PATH
	and path variables are connected - modifying one will actually
	change them both.  Here 'set path = ...' is done, instead of
	'setenv PATH ...' just because the syntax of the former is more
	visually appealing.

	The user should only enter this command once, even if they
	are repeating the entire process.  Repeating this command will
	have the (wasted) effect of adding ~/abin to your path multiple
	times.  To be sure, view the file '~/.cshrc' to make sure that
	the command 'set path = ( $path ~/abin )' appears only once.

	Displaying the contents of ~/.cshrc in the terminal window can
	be done with 'cat ~/.cshrc' or 'more ~/.cshrc'.


    Step 4: log out and log back in

	This is done to invoke the change to the .cshrc file, meaning
	that any new terminal window would have a command shell with
	~/abin in the PATH.  It also has the effect of using the
	'rehash' command, which tells the shell (T-shell) to make note
	of all executables in the PATH.


    Step 5: open a new terminal window, and start playing!
	
	cd AFNI_data1/afni
	afni
	

	Note that if the 'afni' command fails, you may want to review the
	steps that have been taken.  There are two commands that may help
	resolve any problems:
	
	echo $PATH
	rehash
	

	The 'echo $PATH' command will display the value of your PATH variable.
	If your abin directory (like /home/pickle/abin) is not in your PATH,
	and you have logged out and logged back in, then you should review
	updating your ~/.cshrc or ~/.bashrc file, to make sure your abin
	directory is getting added to your PATH.  Go back to 'Step 3'.

	The 'rehash' command will tell the shell about the new programs in
	your path (if your path has been updated, but you haven't logged out
	and back in again).

	Enjoy!