Assumption(s):

    The computer's operating system should be a recent release of Linux.

    The commands listed below assume that the user is running the T-shell
    (/bin/tcsh).  This makes a difference here only when setting the path,
    but in general, /bin/tcsh is recommended over /bin/bash.

    To change the shell to /bin/tcsh, see notes: change the shell

    Note: /bin/tcsh must be installed, even if not as the user's shell.

    To set the PATH under /bin/bash,  see notes: set the PATH in /bin/bash

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Description:

    There are basically 6 steps to installing and running AFNI, though some
    depend on the version of Linux installed.  The commands associated with
    these steps can be entered into a terminal window.

    For a user with very modest experience, it may be best to copy-and-paste
    the commands into a terminal window, rather than to type them in.  If a
    typo is not noticed or understood, it can be difficult to figure out how
    to correct a mistake.

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AFNI: download and install

    Step 0: Install any needed libraries or other packages.  At a minumum
            libXp and tcsh are commonly needed.  Some python packages might
            also be desired, as well as R.
	    
	    sudo yum install libXp tcsh
	    sudo yum install PyQt4 R
	    

    Step 1: Make a home abin directory, where the AFNI binaries will go.
	    
	    cd
	    mkdir abin
	    

    Step 2: Download current binaries.  Since this may vary depending on the
            OS and version, here are some package options:

                1. linux_openmp     : for multi-CPU systems, (needs libgomp)
                2. linux_openmp_64  : 64-bit version of the same
                3. linux_xorg7      : otherwise current linux package
                4. linux_xorg7_64   : 64-bit version of the same
                5. linux_gcc32      : oldie but a goodie
                6. linux_gcc33_64   : similar, but 64-bit

            Choose an appropriate package for the "set package" command.
	    
            set package = linux_openmp_64

	    wget http://afni.nimh.nih.gov/pub/dist/tgz/$package.tgz
	    tar xvfz $package.tgz
	    mv $package/* abin
	    rmdir $package
	    

    Step 3: Add the AFNI package directory ~/abin to your path.  This is only
            done once on a new system.  You can look at the .cshrc file in a
            text editor.
	    
	    echo 'set path = ( $path ~/abin )' >> ~/.cshrc
	    


    Step 4: (optional, but helpful)  Update help files for tab-completion.
            Run this command, and then follow the brief instructions.

            apsearch -update_all_afni_help

    Step 5: Log out and log back in.  This is to make sure that the AFNI 
            programs are recognized in your path.

    Step 6: Start playing!

            afni


    See Class Setup for details on getting the data and handouts needed
    for an AFNI class.