5.1.2. AFNI GUI: Main controller

AFNI GUI: Main controller


Load underlay/overlay datasets

  • An Image Window may have opened when afni was launched. (If not, you can open an image window by clicking Image next to Axial, Sagittal, or Coronal; see here ).

  • UnderLay chooses which 3D dataset to view as the background (grayscale).

    • Current underlay dataset determines the resolution of and 3D region covered by image viewers.

    • anatomical or time series datasets usually go here.

    • Datasets which can be graphed are marked with a * after their names.

  • OverLay Use this to choose which overlay (color) 3D dataset to view.

    • Functional (statistical) dataset usually goes here.

    • Functional datasets will be interpolated to the underlay resolution, and flipped to that orientation (if needed).

      • The Define Datamode panel controls the interpolation method (see here).

  • Both buttons open a dataset chooser window (see here).

  • Datasets that are compressed have a z after their names.

  • Datasets available are from the current session.

  • If new datasets have been added to the current session directory, afni will rescan the directory and popup a little message.

  • See here for more information on the Image Window.


1st column

Coordinate Display

  • The xyz-coordinate display in upper left corner shows current focus location.

  • By default, the coordinates are in RAI order (from the DICOM standard):

    • x = Right (negative) to Left (positive)

    • y = Anterior (negative) to Posterior (positive)

    • z = Inferior (negative) to Superior (positive)

  • This display order can be changed to the neuroscience imaging order LPI:

    • x = Left (negative) to Right (positive)

    • y = Posterior (negative) to Anterior (positive)

    • z = Inferior (negative) to Superior (positive)

    • Right-click in coordinate display to change the coordinate order



  • Xhairs: Type of crosshairs

    • Off: no display of crosshairs

    • Single: display of single crosshairs

    • Multi: display of crosshairs for each slice in the ‘montage’ layouts

    • LR+AP: display crosshairs only parallel to the L-R and A-P axes (etc.)

  • X+: Montage will show the crosshairs in all slices or just one slice.

  • Color: Change the color of crosshairs to make it more visible with certain image overlays.

  • Gap: Size of gap (in voxels) at the center of the crosshairs.

  • Wrap: Montage layout wraps around when the slices go past an edge of the dataset.



  • Index: Time index

    • Controls the time index of the images being viewed.

    • Controls the underlay image only.

    • Only available for images that have multiple subbricks (usually for time).

    • Increment or decrement with the arrows or just type in the number.

    • Right click on Index for a menu of extra options.


Image and Graph

  • Image and Graph buttons for the adjacent views (Axial, Sagittal, Coronal).

    • Normal: button opens a viewing window.

    • Inverted: button raises opened window.

    • Right-click on an inverted button ‘fetches’ the image / graph window.

  • N.B.: AFNI does not read datasets from disk until a window is opened.

  • This can make opening the first viewing window be quite slow

  • Graph buttons are only enabled for datasets that are viewing their data files directly.

    • Not warping on demand – see the top of the Define Datamode control panel (see here).



  • BHelp button: when pressed, the cursor changes to a hand shape.

    • Use it to click on any AFNI button and you will get a small help popup (and click on it when done, to close).

    • AFNI also has ‘hints’ (AKA ‘tooltips’).

  • Press the done button twice within 5 seconds to exit AFNI.

    • The first button press changes done to DONE.

    • Fail to press second time in 5 seconds: it changes back to done.

    • Don’t press a mouse button in the blank square to the right of done. We won’t be responsible for the consequences.


2nd column


  • Use these to select the type of view for your data. Need more here.

    • Original View

    • AC-PC Aligned

    • Talairach View

    • notes on why these are sometimes greyed out.


Overlay and Datamode

  • Define Overlay ->: Use this to control the thresholds, colors, etc. for overlays.

  • See Overlay: Show / Hide the overlay dataset.

    • This is useful for seeing what anatomical features are ‘under’ a particular overlay color.

  • Define Datamode Use this to control the mode in which the underlay data is viewed, and also to save 3D datasets to disk.


DataDir, Switch and Read

  • Switch Use this to choose from which session 3D datasets may be viewed.

    • All datasets in same directory are assumed to be aligned in space.

      • this is in the handout, but I don’t think it is true…

    • Any dataset can be the underlay; any dataset can be the overlay.

  • Read Click this button to get a ‘chooser’ dialog window to select a new directory from which to read datasets.

    • This will add a new ‘session’ that you can select with the Switch button.


EditEnv and NIML+PO

  • EditEnv need more here.

  • NIML+PO: Start listening for NIML and Plugout TCP/IP (network sockets) need more here.

    • Expecting AFNI to talk to suma and/or plugout_drive.

    • Like running afni -niml -yesplugouts on the command line.

    • Greyed out if already listening (you already pushed it or launched afni with -niml -yesplugouts.


Control Surface

  • Control Surface: control the display of overlaid surfaces in the image viewers when talking with suma.

    • Surface nodes will have little boxes drawn, when they appear in a slice.

    • Surface triangles will have line segments drawn, where they intersect a slice center-plane.

    • Greyed out if suma is not running and talking with afni.


News, Forum, Tips, Helps, YouTube


Jump within GUI Guide


Main controller

Image window

Graph window

Overlay panel

Datamode panel

Chooser menu