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!