NeuroElf wiki

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====== NeuroElf - keyboard commands ======

===== Motivation =====
While in principle all functions can be reached via the mouse (using [[neuroelf_gui - menu tree|menu items]] or clicking buttons), it is sometimes "faster" (e.g. by avoiding menu items) or "more precise" (e.g. to select the current position/viewpoint) to use keyboard shortcuts. Below is a list of key bindings to function calls:

===== Requirements =====
To follow this page, you need to have the GUI open by entering ''neuroelf_gui'' at the Matlab prompt.

===== Background information =====
The GUI (and its satellite windows) have the following properties (which can, in part, be manipulated via keyboard commmands):

  * for the slicing view:
    * orientation (either neurological or radiological)
    * current view (either 3-panel or one of sagittal-, coronal-, or axial-only views)
    * current position (the X-/Y-/Z- coordinate at which the slicing planes are defined)
    * current volume (or timepoint) of 4D data (fixed at 1 when a 3D dataset is displayed)
    * crosshair display (on or off)
    * currently selected anatomical dataset/object (first dataset dropdown)
    * currently selected statistical dataset/object (second dataset dropdown)
    * currently selected maps from the statistical object (listbox of available maps)
    * statistics settings (tails, value-based thresholding, cluster thresholding on or off, transparency setting, joining or overpainting)
    * interpolation setting (on or off, type of interpolation either linear or cubic)
    * drawing mode (on or off, intensity or undo drawing, drawing-over range definition, brush size and shape, as well as 2D or 3D drawing; **VMR/HDR only**)
    * potentially linked [[neuroelf_gui - GLM beta plotter|GLM beta plotter]] UIs (main UI only)
  * for the surface view
    * viewpoint settings (as defined by azimuth and zenith angles, as well as X- and Y- translation along the viewing plane and a scaling factor)
    * currently shown surface objects (scenery listbox)
    * for each shown surface object the currently selected statistical object (configurable on the currently selected surface object only)
    * for each selected statistical object the currently selected maps
    * statistics setting (tails, value-based thresholding, surface cluster size thresholding on or off, transparency setting)
    * for each shown surface object a setup definition (faces or wireframe, transformation)

===== Main UI =====

==== Slicing view ====
  * orientation - **O**: toggle between neurological and radiological viewing mode
  * current view - **T**: cycle through the 4 view types (3-panel, sagittal, coronal, axial)
  * current position
    * **cursor -left/-right**: alter current position by decreasing (cursor-left) or increasing (cursor-right) the X-coordinate by 1mm (for 0.5mm-resolution VMRs: 0.5mm), thus altering the sagittal slice view
    * **cursor -up/-down**: alter current position by increasing (cursor-up) or decreasing (cursor-down) the Z-coordinate by 1mm (for 0.5mm-resolution VMRs: 0.5mm), thus altering the axial slice view
    * **//SHIFT +// cursor -up/-down**: alter current position by increasing (cursor-up) or decreasing (cursor-down) the Y-coordinate by 1mm (for 0.5mm-resolution VMRs: 0.5mm), thus altering the coronal slice view
  * current volume - **//SHIFT +// cursor -left/-right**: decrease (cursor-left) or increase (cursor-right) current volume by 1
  * crosshair display - **A**: toggle crosshair display between on and off
  * currently selected dataset - **//CTRL +// S**: select next available dataset for display (in the order they are listed in the dropdown)
  * currently selected map - **//SHIFT +// M**: select next available map from container (only works if exactly one map is selected)
  * statistics settings
    * **1**/**2**: en-/ disable positive (1) and negative (2) tail of the currently selected (single) voxel-based map
    * **C**/**K**: toggle cluster-size based (k-) thresholding between on and off
    * **N**: negate alpha (transparency) value setting (in effect toggling the alpha-by-stats-value scaling between on and off)
    * **//ALT +// cursor -up/-down**: increase (cursor-up) or decrease (cursor-down) alpha setting value by 0.1, if value is negative, scale transparency by statistical value
    * **J**: toggle between map-joining and map-overpainting mode (if joined colors will be mixed, otherwise maps appearing later in the list have precedence over earlier maps)
  * interpolation
    * **I**: toggle interpolation setting between on and off
    * **M**: toggle interpolation mode between linear and cubic
  * drawing mode
    * **B**: switch drawing off (browse-mode)
    * **U**: toggle between regular (intensity value) and undo (from-buffer) drawing modes
    * **D**/**3**: switch drawing on and enable 2D (D) or 3D (3) drawing mode (within selected slice only)

==== Surface view ====
  * viewpoint
    * **cursor -left/-right**: increase (cursor-left, left-rotate) or decrease (cursor-right, right-rotate) azimuth angle of viewpoint by 5 degrees (between 0 and 360)
    * **cursor -up/-down**: decrease (cursor-up, up-rotate) or increase (cursor-down, down-rotate) zenith angle of viewpoint by 5 degrees (up to +/- 90)
    * **//SHIFT +// cursor -left/-right**: decrease (cursor-left, shift-left) or increase (cursor-right, shift-right) X-translation of viewpoint by 5mm (unrestricted)
    * **//SHIFT +// cursor -up/-down**: increase (cursor-up, shift-up) or decrease (cursor-down, shift-down) Y-translation of viewpoint by 5mm (unrestricted)
    * **//CTRL +// cursor -up/-down**: increase (cursor-up, zoom) or decrease (cursor-down, unzoom) scaling/zoom factor by factor 0.01 (unrestricted)
  * currently selected map - **//SHIFT +// M**: select next available map from container (only works if exactly one map is selected)
  * statistics settings
    * **1**/**2**: en-/ disable positive (1) and negative (2) tail of the currently selected (single) voxel-based map
    * **C**/**K**: toggle cluster-size based (k-) thresholding between on and off
    * **J**: toggle between map-joining and map-overpainting mode (if joined colors will be mixed, otherwise maps appearing later in the list have precedence over earlier maps)

==== Global settings and functions ====
  * **L**: toggle between local-maximum splitting setting on and off (when using the Clustertable button)
  * **R**: reset viewmode (orientation to neurological, current position to 0, 0, 0; interpolation method to cubic, painting mode to regular, viewpoint to default settings, stats transparency alpha to 1)
  * **S**: toggle between full-size and reduced-size modes
  * **X**: toggle between auto-cluster extraction modes on and off (if on, selecting a cluster from the list of VOIs will automatically extract betas from a selected GLM)
  * **Z**: toggle between zoomed and un-zoomed view (in the slicing views)
  * **//CTRL +// L**: toggle between linked and un-linked browsing
  * **//CTRL +// R**: reset transformation matrix of currently selected sliced object to the identity matrix (no additional transformation)

===== Satellite UI =====
Orientation, current view, current position/viewpoint, current volume, crosshair display, currently selected map, interpolation and across-window-linking can be configured as with the main UI. Additionally, the following keyboard shortcuts are available:

  * **//SHIFT +// S**: save a screenshot as either BMP, JPG, PNG, or EPS (for high-quality images, particularly for surfaces, e.g. via Photoshop or GIMP rendering)

===== Alphabetical list =====
This list does **not** contain cursor commands!

  * **A**: toggle crosshair display between on and off (main UI and satellites, slicing view only)
  * **B**: switch drawing off (browse-mode) (main UI only, slicing view only)
  * **C**: toggle cluster-size based (k-) thresholding between on and off (main UI only, slicing and surface views)