.. _edu_afni03_main: ***************************** **AFNI GUI: Main controller** ***************************** .. contents:: :local: .. list-table:: :header-rows: 1 :width: 40% :align: center * - AFNI GUI: Main controller * - .. image:: media/afni_controller_window.png :width: 100% :align: center .. _gui_guide_main_load_dsets: Load underlay/overlay datasets ============================== .. list-table:: :widths: 60 40 :header-rows: 0 * - * 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``; :ref:`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 (:ref:`see here`). * Both buttons open a dataset chooser window (:ref:`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. * :ref:`See here for more information on the Image Window`. - .. image:: media/afni_controller_window_under_over_lay.png :width: 100% :align: right 1st column ================= .. _gui_guide_controller_window_xyz: .. list-table:: :widths: 60 40 :header-rows: 1 * - :ref:`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 - .. image:: media/afni_controller_window_xyz.png :width: 100% :align: right .. _gui_guide_controller_window_xhairs: .. list-table:: :widths: 60 40 :header-rows: 1 * - :ref:`Xhairs` - * - * ``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. - .. image:: media/afni_controller_window_xhairs.png :width: 100% :align: right .. _gui_guide_controller_window_Index: .. list-table:: :widths: 60 40 :header-rows: 1 * - :ref:`Index` - * - * ``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:: media/afni_controller_window_index.png :width: 100% :align: right .. _Open Image and Graph: .. _gui_guide_controller_window_image_graph: .. list-table:: :widths: 60 40 :header-rows: 1 * - :ref:`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 :ref:`(see here)`. - .. image:: media/afni_controller_window_image_graph.png :width: 100% :align: right .. _gui_guide_controller_window_BHelp: .. list-table:: :widths: 60 40 :header-rows: 1 * - :ref:`BHelp` - * - * ``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. - .. image:: media/afni_controller_window_bhelp_done.png :width: 100% :align: right 2nd column ============== .. _gui_guide_controller_window_Views: .. list-table:: :widths: 60 40 :header-rows: 1 * - :ref:`Views` - * - * 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. - .. image:: media/afni_controller_window_view.png :width: 100% :align: right .. _gui_guide_controller_window_Overlay_Datamode: .. list-table:: :widths: 60 40 :header-rows: 1 * - :ref:`Overlay and Datamode` - * - * ``Define Overlay ->``: Use this to control the thresholds, colors, etc. for overlays. * More on this here -> :ref:`Overlay`. * ``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. * More on this here -> :ref:`Datamode`. - .. image:: media/afni_controller_window_overlay_datamode.png :width: 100% :align: right .. _gui_guide_controller_window_DataDir: .. list-table:: :widths: 60 40 :header-rows: 1 * - :ref:`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. - .. image:: media/afni_controller_window_DataDir.png :width: 100% :align: right .. _gui_guide_controller_window_EditEnv_NIML: .. list-table:: :widths: 60 40 :header-rows: 1 * - :ref:`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``. - .. image:: media/afni_controller_window_env_niml.png :width: 100% :align: right .. _gui_guide_controller_window_ControlSurface: .. list-table:: :widths: 60 40 :header-rows: 1 * - :ref:`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``. - .. image:: media/afni_controller_window_cont_surf.png :width: 100% :align: right .. _gui_guide_controller_window_NewsForum_etc: .. list-table:: :widths: 60 40 :header-rows: 1 * - :ref:`News, Forum, Tips, Helps, YouTube` - * - * Green buttons open your default web browser to various afni related pages. * Blue button opens an afni GUI window with lots of info. * ``News``: Web link to `AFNI Digest History `_. * ``Forum``: Web link to `AFNI Message Board `_. * ``Tips``: GUI window with lots of info. A web based version of this exists `here `_. * ``Helps``: Web link to `All program helps `_. * ``YouTube``: Web link to the official `"AFNI Academy" YouTube page of Bootcamp lecture videos `_. - .. image:: media/afni_controller_window_news_etc.png :width: 100% :align: right Jump within GUI Guide ======================== .. include:: substep_gui_jump.rst