Displaying Image Data Values as Colours

Rview allows multiple data sets to be displayed together using various simple graphical techniques in a common 3D image space. In its simplest form there is a reference image and one or more 'floating' images. Each of the data sets loaded into rview are displayed with a separate colour map as shown below:
colour display
 

Colour Map Control


In order to display medical image data values on the screen we must map voxel values (i.e. CT values or Hounsfield Units, SPECT voxel counts or MR signal) to screen pixel colours. This is achieved using a linear lookup table control for each volume data set. Because most medical image data has a large dynamic range (e.g. 10-16 bits) compared to the number of levels you can see on your monitor you will usually have to adjust the range of data values mapped to this colour scale. (Because of the great variety of monitors and monitor settings these values may well be very different on different PC's). The pixel colours used to display the selected range of data values are controlled by the individual colour tables for the Reference, and floating image (Image A, Image B... etc.) menus:

This provides a pop-up to select a range of grey and simple colour scales as well as a number of standard colour tables used in nuclear medicine:

cd
Colour Selector Dialogue for Reference Image Data

This is split into a number of separate functional areas. The graphs on the right hand side of the tool shows (from top to bottom) the RGB values mapping over the currently selected data range, the opacity map and, at the bottom, the histogram of the whole volume within the currently selected data range. Thus, in the above example, everything below 8 is mapped to black, everything above 180 is mapped to white and between these values is a grey scale. Finally, at the bottom of this section, the histogram shows, for example, the peaks of grey matter, white matter and AIR/CSF:

cmapEG

Text Input of Data Range

The most direct and precise method of setting the displayed range of image data values is provided by interactive text input on the Colour Tool (See above) for each data set. Here the Max and Min Values:

min max

defining the range can be entered manually. On pressing return, the display is updated using this data range. The "Auto Scale" option re-calculates the range from the image data using a statistically derived fraction of the full range of the image data volume. The CT options set different pre-set ranges applicable to CT data loaded in CT units. The Arrow controls on the right allow the control to be changed to different datasets (seg Reference, Floating Image A, B etc).

On Screen Display Range Control

The simplest and most direct approach to modifying the data range displayed is to use the on-screen colour map controls which are displayed along the bottom of the display window:
 

 

Each control consists of a minimum and maximum numerical value displayed at the left and right respectively (same as in the respective colour tool range). Between these numbers is a scale of ticks representing the full range of data values present in the data. (When loading the volume image, rview finds the maximum and minimum values in the entire volume.) On top of this scale is a grey (black to white) or colour scale. In the above figure: all values above 1165 are displayed as white, while all values offer and below are displayed as black. When the mouse cursor is moved into this area it changes to a vertical split line as shown in the figure. To reduce the maximum value:

It is important to note that when clicking on the scale, the minimum or maximum colour value is selected depending on which is NEAREST to the mouse. If the maximum and minimum are close together, click above or below to move the maximum or minimum scale point up or down.  

Signed Symmetric (Subtraction) Colour Scales

If a subtraction image is being viewed a signed colour scale may be selected. This provides symmetric control over the display of positive and negative changes between two images. These colour scales have black in the middle corresponding to zero change and a range of other colours for positive and negative changes. These signed colour scales are displayed on the main display window as a split scale:

Here the range 92 to 1086 has been selected. The upper colour scale represents the numbers in this positive range (black on the left corresponding to '92' or below). While the lower colour range represents the colours for the data values -1086 up to -92 (black). Everything between -92 and 92 is displayed as black.


Symmetric Colour Scales

Gamma Control In addition to a simple linear mapping it is possible to modify the gamma function mapping data to colour pixel values. In particular each modality is displayed using a separate gamma function. The gamma function for each data set is controlled by individual gamma settings on the colour tool dialogue:
 
As for the data range control, pressing Enter [return] redraws the current display with that gamma setting.
 

Getting a Good Contrast Display:

As a rough guide to getting a good display of typical raw MRI or SPECT data of the brain, the maximum display value may be brought down to about 80% of the maximum value present in the data. In addition the minimum value may be increased from zero to about 10% of the maximum range.

The following sections illustrate the process of setting up a fused MRI-PET/SPECT display.

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