================================================================================
                ----===|  Usage Tips for the AFNI GUI  |===----
================================================================================
Tip #1:
  When the AFNI sunrise logo is displayed in the square to right of the 'done'
  button, this means that something is happening that might take a long time
  (e.g., reading a big file).  The AFNI GUI will not respond to clicks or
  keystrokes during this time.
--------------------------------------------------------------------------------
                    ***** AFNI For Absolute Beginners *****

(1) To use AFNI, you must have some data stored in a format that the program
    understands.
  (a) The major formats for which AFNI is programmed are:
       ++ AFNI formatted datasets, in .HEAD and .BRIK pairs of files;
       ++ NIfTI-1 formatted datasets, in .nii or .nii.gz files.
  (b) When you start AFNI, any datasets in the current directory will be ready
      for viewing.  If there are no datasets to read, AFNI will pop up a
      message.  At this point, you can do one of 2 things:
       ++ Quit AFNI, change directory ('cd') to a directory with some datasets,
          and restart the program (this is what I always do); or,
       ++ Use the 'DataDir Read' button in the second column of the main AFNI
          controller to navigate to a directory with some datasets.
      When there is no data, AFNI creates a 'dummy' dataset for you to look at,
      if you want to play with the image viewers.
  (c) To open an image viewer, click on one of the 'Image' buttons in the left
      column of the main AFNI controller.
       ++ Left-click in the image to move the crosshairs around.
       ++ Click or click-drag in the slider below the image to change slice.
       ++ The controls to the right of the image let you adjust the image
          contrast, brightness, zoom factor, etc.
       ++ The controls to the bottom of the image let you carry out various
          operations on the image, such as saving to JPEG format, and making
          a montage (array) of slice images.
  (d) If a dataset has more than one 3D volume in it (usually that means it
      has a time axis, like an FMRI EPI dataset), then you can use the 'Graph'
      buttons to view an array of graphs of the voxel data time series.
       ++ The crosshairs in the image viewer that corresponds to the graph
          viewer change to a small box to indicate which voxels are the source
          of the data in the graph array.
  (e) The viewpoint of multiple image and graph viewers (the focus voxel at the
      crosshairs) is always locked together -- Left-click in one image to move
      the crosshairs, and all other open image and graph viewers will jump, too.
       ++ Moving the time index in a graph viewer (by clicking in the central
          sub-graph, or by using the 'Index' control in the main AFNI window)
          will cause all the image and graph viewers to display at the new
          time index.
  (f) At any moment, you can have one underlay dataset (grayscale) and one
      overlay dataset (color).  To choose which datasets are visible, use
      the 'UnderLay' and 'OverLay' button in the second column of the AFNI
      controller.
       ++ To control whether the color overlay is visible, click on the 
          'See OverLay' toggle button.
       ++ To manage how the numbers in the overlay dataset are converted into
          colors, click on 'Define OverLay' to open up a new control panel.
       ++ The active underlay and overlay dataset names are shown in the title
          bar of the AFNI controller window.
  (g) Don't be afraid of the software!  The popup hints will help.  The button
      'BHelp' will give you longer help about individual buttons -- click on
      the BHelp button, then click on any AFNI button to get a small text box
      with more help than the simple popup hints.
  (h) Sample datasets and all the AFNI course materials are in the big file
      CD.tgz (more than 1 Gbyte) at
         http://afni.nimh.nih.gov/pub/dist/edu/data
      And don't forget the AFNI message board at
         http://afni.nimh.nih.gov/afni/community/board
--------------------------------------------------------------------------------
             ***** Cursor Shapes and Right-Click Popup Menus *****

(2) On most systems, the X11 cursor used in AFNI is an orange arrow pointing
    at about '10:30' on the clock face.  However, the arrow becomes yellow
    and points more steeply, to about '11:00', when it is over a location that
    has a hidden Right-Click popup menu.  Some of these are
   (a) Over the logo square just to the right of the 'done' button in an
       AFNI controller.
   (b) Over the labels at the top of the threshold slider and color bar in
       the 'Define Overlay' control panel.
   (c) On the label to the left of a drop-down 'option menu'; e.g., 'Xhairs'
       or 'ULay' (for these menus, the cursor will not change shape).
   (d) Over the color bar itself, when it is in continuous 'colorscale' mode
       ('**') -- but not when it is in discrete color panel mode.
   (e) Over the image viewer main sub-window, which holds the image itself.
   (f) Over the image viewer intensity bar, just to the right of the image.
   (g) Over the 'Save' button in the image viewer.
   (h) Over the 'crop' button in the image viewer.
   (i) Over the sub-graphs in the time series dataset graph viewer
       (pops up some statistics about the data in the sub-graph).
   (j) Over the coordinate display in the upper left corner of an AFNI
       controller.
   (k) In the 'Render Dataset' plugin, over the 'See Xhairs' and 'Accumulate'
       toggle buttons.  The 'Accumulate' popup lets you enter a text label
       to be drawn in the rendered image viewer -- the actual display of labels
       (size and location) is controlled from the image viewer intensity bar
       popup menu -- item (e) above.  Right-Click lets you change the label
       for newly rendered images, whereas Shift+Right-Click lets you change
       the label for all previously rendered images as well as new images.
   (l) In the 'Clusters' report panel, right-clicking in the upper part of
       the window (where the textual summary is), will let you choose how
       the 'Histog' option will plot the histogram from the 'Aux.Dset'.
       ('Histog' is selected from the menu whose initial choice is 'Mean'.)
--------------------------------------------------------------------------------
              ***** Hidden Clicks to Activate AFNI Features *****

(3) Other 'special' clicks that aren't obvious:
   (a) Left-clicking on the 'Image' or 'Graph' button for an already open
       AFNI viewer will bring that viewer's window back up to the top of
       the X11 window stacking order.
   (b) Right-clicking on the 'Image' or 'Graph' button for an already open
       AFNI viewer will bring that viewer's window over to the place where
       you just clicked -- this is useful for finding lost viewers.
   (c) Right-clicking on the 'DataDir' button in the AFNI controller will
       un-hide (or re-hide) the obsolescent 'Define Markers' button.
   (d) Left-clicking on the logo at the lower left of a graph viewer will
       make the logo and menu buttons disappear -- this is intended to help
       you make a clean-looking snapshot of the window.  Left-click again
       in the same region at the lower left to un-hide the logo and buttons.
   (e) Right-clicking on the graph viewer logo or on the image viewer 'Disp'
       button (i.e., the things at the lower left of each viewer window) will
       bring the parent AFNI controller back to the top of the X11 window
       stacking order.
   (f) In an image viewer window, if you press-and-hold-down the Left mouse
       button, then drag the cursor vertically and horizontally (while still
       holding the Left button down), the contrast and brightness of the
       grayscale underlay changes as you move the mouse.
   (g) To exit AFNI quickly when multiple controllers are open, hold down the
       Shift key when you press the 'done' button (in any AFNI controller).
       The usual requirement of pressing 'done' twice within 5 second is
       skipped, and all AFNI controllers exit immediately.
   (h) Left-clicking in the logo square to the right of the AFNI controller
       'done' button will cause the AFNI splash screen to popup.  You can
       close the splash screen window again via the usual X11 controls on
       the window border, or by left-clicking again in the logo square.
--------------------------------------------------------------------------------
               ***** Keyboard Shorcuts: Image Viewer Window *****

(4) The AFNI image viewer has many keyboard shortcuts.  Help for these can be
    found by using 'BHelp' and then clicking on the image sub-window itself.
    The shortcuts are used by putting the mouse cursor over the image sub-window
    and pressing the keyboard key.
      a = fix window aspect ratio        (= Left-click in intensity bar)
      c = enter cropping mode            (= clicking the 'crop' button)
      D = open Disp control panel        (= clicking the 'Disp' button)
      i = make the image sub-window smaller inside the overall viewer
      I = make the image sub-window larger
      l = left-right mirror image        (= '+LR Mirror' on Disp panel)
      m = toggle 'Min-to-Max' on/off     (= 'Min-to-Max' or '2%-to-98%' on Disp)
      M = open Montage control panel     (= clicking the 'Mont' button)
      o = color Overlay on/off           (= 'See Overlay' in AFNI controller)
      p = toggle panning mode            (= clicking the 'pan' button)
      q = close window                   (= clicking the 'done' button)
      r = like 'v', but image 'rebounds' when it reaches end of count
      R = like 'r', but backwards order
      s = sharpen underlay image         (= 'Sharpen' on the Disp control panel)
      S = save image                     (= clicking the 'Save' button)
      u = toggle background to be from Underlay or Overlay dataset
      v = automatically change images to make a 'video' (forwards order)
      V = same as 'v' but backwards order
      z = zoom out                       (= zoom down-arrow button)
      Z = zoom in                        (= zoom up-arrow button)
      [ = time index down by 1
      ] = time index up by 1
      { = lower AFNI statistical threshold slider
      } = raise AFNI statistical threshold slider
      > = PageUp = move forward one slice in image viewer
      < = PageDown = move backward one slice in image viewer
      # = toggle checkerboard pattern from underlay and overlay datasets
      3 = turn checkerboard pattern off
    Keyboard arrow keys = move crosshairs (normal operation)
                        = pan zoomed window (when 'pan' is on)
    Shift+arrow keys    = pan cropped region around
    Ctrl+arrow keys     = expand/shrink cropped region
    Home key            = center zoomed window on current crosshair location
    Shift+Home          = center cropped region on current crosshair location
    Del = undo in the Drawing plugin
     F2 = turn the Drawing pencil on
     F3 = subtract 1 from the Drawing plugin value
     F4 = add 1 to the Drawing plugin value
     F5 = Meltdown!
     F6 and higher are not (yet) defined.
--------------------------------------------------------------------------------
               ***** Keyboard Shorcuts: Graph Viewer Window *****

(5) The AFNI graph viewer also has many keyboard shortcuts.
      a = autoscale the graphs (this one time)
      A = autoscale the graphs (every time they are redrawn)
      b = switch graph baseline mode (between Separate, Common, and Global)
      B = switch on/off Boxes graphs instead of line graphs
      g = decrease vertical grid spacing in graphs
      G = increase vertical grid spacing in graphs
      h = draw dotted horizontal line at zero level in graphs
      i = decrease graph 'ignore' level by 1
      I = increase graph 'ignore' level by 1
      l = move to last time point
      L = turn AFNI logo on or off (but why would you want it OFF?!)
      m = reduce matrix size of sub-graphs by 1
      M = increase matrix size of sub-graphs by 1
      q = quit = Opt->Done
    r/R = 'rebound' up or down in time
      S = save an image of the graph window to a file
      t = show text (numbers) instead of graphs
    v/V = 'video' up or down in time
      w = write data from central sub-graph to a 1D file
      z = change slice number by 1 downwards (= keyboard Page Down key)
      Z = change slice number by 1 upwards   (= keyboard Page Up key)
      - = scale the graphs down (vertically)
      + = scale the graphs up
      1 = move to first time point
 < or [ = move back in time by 1 point  (= keyboard Left arrow)
 > or ] = move up in time by 1 point    (= keyboard Right arrow)
      N = after typing the 'N', type a number, then press Enter;
          the matrix of sub-graphs will change to the number given immediately
     F5 = Meltdown!
--------------------------------------------------------------------------------
            ***** Keyboard Shortcuts in the Threshold Slider *****

(6) Fine control over the threshold slider is hard with the mouse.  You can
    move the slider with the following keystrokes, after clicking in the
    slider's 'thumb' to move the keyboard input focus to this control.
      Down arrow = reduce slider by 1 in the 4th significant place
      Up arrow   = increase slider by 1 in the 4th significant place
      Page Down  = reduce slider by 1 in the 3rd significant place
      Page Up    = increase slider by 1 in the 3rd significant place
      Home       = drop slider to 0
      End        = move slider to top
    The Left and Right arrow keys can similarly be used in the image viewer
    slice index slider to move 1 slice backward or forward at a time.
--------------------------------------------------------------------------------
