
Open the afni GUI (graphical user interface) in the results directory.

We are not quite ready to look at the results, but since we are moving our
attention to the results directory, it seems a conceptually good time to start
afni and refer to it later.

We should still be sitting in the FT_analysis directory.  Verify this with the
'pwd' command (it should output something like .../AFNI_data6/FT_analysis).

      % pwd

      % cd FT.results
      % afni &

Recall that the '&' after the 'afni' command puts afni in the background.
That means we can still run commands (like 'ls') in that terminal window, even
though afni is now running.  Recall also that if 'afni' is started in the
foreground (i.e. without the '&'), that it can be be put in the background by
using ctrl-z, followed by 'bg'.

In that case:

   The ctrl-z keystroke suspends afni and gives the terminal back to the user.
   Note that the afni window is not currently responsive to button presses
   (though they may be stored for later).  Running the 'bg' command tells the
   shell to let afni continue to run but in the background, again, leaving the
   terminal open for more commands.

   Note that once 'bg' is entered, afni may apply the button presses that were
   made while it was suspended.

----

How will we tend to look at the data in afni?

   At each processing block, we will look at "before" and "after" pictures of
   the EPI data.  We may care about the images, the time series or both.  So
   along the top half of the screen open axial Image and Graph windows.  This
   is done on the top half of the screen to save the bottom half for another
   set of windows (an afni controller and Image and Graph windows).

   Note: this is also done to save screen space in class (since laptops do
         not have so much.  Of course, it is nicer to open more windows.

   Load run 1 of the initial EPI data and as before, jump to xyz coordinate
   (19.3 78 -5.7).

        - change Underlay to pb00.FT.r01.tcat
        - open Axial Image and Graph windows (along top of display)
        - in the Axial image window, right-click, "Jump to (xyz)"
        - enter the coordinates 19.3 78 -5.7 and click Set

        - in the Graph window type 'A' to Autoscale (or Opt->Scale->AUTO)

          --> the terminal window should show the resulting output:

                ++ Graph Viewer: Autoscale forced ON


We will come back to afni later...
