Viewer - cerr/CERR GitHub Wiki

CERR's Viewer is used to review volumetric data - scans (CT, PET, MRI, SPECT, Gamma-Knife), dose distributions, anatomical structures, and gray scale presentation state annotations (GSPS). The Viewer can display transverse, sagittal and coronal images simultaneously with or without dose overlay. The controls for various operations (e.g. zoom, slice change etc.) can be accessed from the left panel, the menu-bar on the top of the figure, and by right-clicking to bring up the menu for each view.

How to's

  • Launch the viewer
  • Source-code version: Add all CERR files and folders to the MATLAB path. Then invoke CERR by typing 'CERR' into the command line. Click the 'Viewer' button to launch the viewer.
  • Compiled version: After installing the run-time libraries, run CERR.exe. Then click the 'Viewer' button.
  • Load a new archive

Launch CERR's Viewer, then select 'Open...' from the File-menu and select the desired .mat or .bz2 archive to be loaded into CERR.

  • Figure out which view is currently active?

The active view will have its coordinates listed in green text, whereas other views have them listed in yellow text. A view can be made active by left-clicking on it once.

  • Navigate across slices?

There are three ways to do this: (1) Plane locators show where each view is located with respect to the others. Drag the plane locators to show different slices. (2) Use the up and down arrow keys to show different slices of the active view. (3) Use the S+ and S- buttons located on the left panel to show different slices on the active view. (4) Use the mouse scroll wheel to scroll across slices. (5) Click and drag on a view to scroll across slices.

  • Change transparency between scan and dose

The Scan/Dose slider located above the colorbar can be adjusted to obtain the desired transparency. This dynamic color bar allows for easy cutoff and rescaling of the colors used for dose display by dragging the triangles at the edges of the colorbar. Double-clicke the colorbar to set the dose-display range, colorbar display range, and colormap.

  • Change the layout of views

Select ‘Panel Layout’ from the ‘View’ drop-down menu and select the layout you want.

  • Switch between views

Double-click on a non-active view to swap it with the active view (green label).

  • Zoom in and out

Click on the magnifying glass with the + sign. Your cursor will turn into a +. Click on the figure and draw a box around the area you want to zoom in on. When you are done click the magnifying glass with the + sign to turn off Zoom mode. You can click the magnifying glass with the curved arrow to return to the original size

  • Adjust scan contrast

This can be done in two ways: (1) Type in the window center and width on the text boxes located in the left panel. (2) Click the "L" button on the left panel and click and drag on a view to change its center and width simultaneously.

  • Turn off or toggle between scans

Right click on a view and select one of the options listed under 'Scanset' to be displayed on that view .

  • Turn off or toggle between doses

Go to the 'Dose' drop down menu and pick the dose you want to view. You can also right click on a view and select the dose you want to display just for that view.

  • Turn off or toggle between anatomical structures

Right click on a view and select one of the options listed under 'StructSet' to be displayed on that view .

  • Use the legend

Toggle structures on/off by clicking once on the structure's name listed in the Legend panel.