--- AFNI Interactive steps (watch instructor, then do on your own) ---
A. Starting up
  1. Starting AFNI (cd ~/AFNI_data3/afni ; ls ; afni &)
     ----> change to the correct directory and verify there are datasets
  2. Selecting datasets (anat+orig) and display them
  3. Oops, I've got a backwards R in my image viewer

B. Understanding the Underlay and the Image Viewer
  1. Orthogonal views
     - Axial, Sagittal, Coronal planes
     - Crosshairs, coordinates and interactions
     - Navigating the volume with sliders
     - Fine control
     - Voxel values
     ----> Explore space with the various slider, mouse, cursor controls
  2. Display window controls
     - Stretching size and fixing the aspect
     - Color scale controls - brightness, contrast, gamma, color, swap, norm
     ----> Practice adjusting the image
      (Hint: right-clicking on the colorbar and selecting Display Graymap Plot
       can help give a better understanding of the controls and their effects)
     - Getting help - button help, finding out what's right
     - Display scaling (2-98, min-max, clipped, custom)
     - Video and ricochet and changing the environment
     ----> Edit the environment by right clicking a display window.
        In the AFNI Environmentalism menu, adjust AFNI_VIDEO_DELAY to
        various delays in ms. Try video and ricochet with each.
     - Zoom, pan, crop
  3. Saving pictures for later
     ----> save sagittal slice 133 as a jpeg file
     ----> save axial slices 50-100 as animated gif file for your webpage
  4. Seeing more slices at a time with montages
  5. Seeing more data with multiple controllers (select func_slim+orig) 
     - Lock and unlock controllers together
  6. Jump to specific places in the data 
     ----> (x,y,z = -8.9, 9.9, 26; 0,0,0; i,j,k = 0,0,0, jump back)
        Did the coordinates change in the way you expected?

C. Overjoyed with the overlay
  1. Selecting data for overlay (select func_slim+orig)
  2. Overlay colors
  3. Thresholding
     - overlay and threshold sub-brick selection
     - threshold ranges
     - p-values
     ----> Look for the voxel that has the best Full F-stat
        What is the p-value at that voxel?
        What are the coordinates?
  4. More color choices - discrete bands, colorscales, manual ranges,
     voxel values
  5. Opacity
  6. EPI over anatomical data (select epi_r1+orig for overlay)
     ----> evaluate the alignment of the anatomical with the EPI
     using thresholding, opacity, underlay and overlay toggles
     Change color bar to have 10 color panes
     Compare coverage areas, voxel sizes, intensities (bright and dark)
  7. Turn off overlay for now
   
D. Graphic graphing
  1. Dynamic data - load an EPI time series (select epi_r1+orig)
  2. Graph scaling and number of graphs. Ignoring time.
  3. Traveling through time
     - arrows, mouse, <>, [], index selection, video and ricochet
  4. Looking for quality - motion detection
     ----> Remember that outlier at TR 42 in the to3d lecture, investigate
        using the graphs and the image display
  5. Looking at activation
     - select overlay to be func_slim+orig
     - graph ideal with FIM, Pick Ideal. Select epi_r1_ideal.1D.
     ----> Find voxels with higher activation based on Full F-Stat values
        using the graphs
        The experiment has 3 different stimuli in this block design.
        Can you see an effect at any voxel? Nearby voxels? 
        What do the graphs at most voxels look like?
  6. Saving graph data
     ----> Save the graph data for the single voxel with the highest F-stat
        to a file using the 'w' and repeat

E. Plugged-in
  1. Examining voxel values with histogram (anat+orig)
     ----> Using the histogram plug-in, look at the distribution of voxel
        values in the anat+orig dataset. Use 100 bins and try various lower
        and upper limits.
        Are there groups of voxels visible in the histogram plot?
 
F. Datamode and miscellaneous
  1. Finding out more about your data
     ----> Using the Misc, Ulay info and Olay info functions, determine
        the storage order (RAI,LPI,...), voxel size, number of sub-bricks,
        data type and history
        How was anat+orig created?
        Where might you look to see if data has already been smoothed or
        volume registered?
  2. Oops, my dataset's not showing up in the underlay or overlay chooser
     -rescanning
     ----> Create a new dataset in a terminal with this command:
       3dTstat -prefix realmean epi_r1+orig
       Make it the new overlay dataset using Rescanth
     -reading and setting new sessions



G. Extra time
  1. Talairach views 
     -switching views
     -whereami
     -showing atlas regions
     ----> Explore atlas regions for "talairached" data
     (Underlay: anat+orig, overlay: funcslim+orig, axial slice 51->61)
     Use whereami to find where the current voxel lies in an atlas
     Color the hippocampus using the right click "Show Atlas" and 
     "Talairach to" it. Turn off atlas colors in Overlay panel.
  2. Giving your data a little nudge (anat+orig)
  3. Comparing data with a scatterplot (anat1+orig, anat2+orig)
  4. SUMA can't talk to AFNI
  5. Controlling the display a bit more 
     ----> Manipulate the image display some more
       (Underlay: anat+orig, overlay: funcslim+orig, axial slice 51)
       Define Datamode, Olay and Stat resam mode to Cu instead of NN
       Can you see the effect on the overlay image and the thresholding?
       Define Datamode, Misc, Edit Environment, 
        AFNI_IMAGE_ZOOM_NN to YES, AFNI_KEEP_PANNING to YES
       Zoom with these new settings

H. Bye
    ----> Click on Done, Double-click Done or Shift-click Done to close all
       Any questions or concerns?