The 'Graphics shader' selection changes the way that surfaces are displayed in the 3D window. The following shaders are available so long as your display drivers at least support OpenGL 3.0:
The 'translucent layers' slider affects visualisation of any non-opaque surfaces or reslices. Anything above zero will correctly display that number of overlapping translucent layers, counting from front to back from each display pixel, as well as any opaque surfaces. Setting this to zero (or on displays not supporting it) will default to a fake translucency which simply displays back surfaces in increasing order of opaqueness, then front surfaces in the reverse order. This was the default before version 7.0.
Note that the 'translucent layers' slider must be non-zero for correctly displaying any non-opaque surfaces mixed in with a
The 'focus range' and 'focus depth' sliders enable simulation of lens focus (depth-of-field) in the 3D window. If the focus range is set to 'large' (all the way to the left), then the entire data is in focus: this is the default setting. However, more realistic visualisations can be created by using a slightly reduced focus range (slider more towards the right), although this will naturally also reduce the sharpness of some features in the window. In this case, the focus depth sets the position at which the lens is focussed, i.e. the sharpest visualistion is created. This simulation is only ever used if a surface or volume rendering is visible, but when it is used, it applies to all features in the 3D window.
The 'background' option allows you to define what colour you wish to use for the background (non-data) parts of any of the data windows. The default is dark grey, but this can be set to any other colour. If the 'uniform' box is not ticked, the background in the 3D window will be appropriately shaded given the amount and direction of the ambient and radiant light, and the viewing perspective. This makes the background match the shaded surfaces better. However, if you want to print screenshots of any of the windows, it may be better to set the background to 'white' and tick the 'uniform' box. The background must also be uniform if you want to grab 3D images including transparency.
Note that the perspective in the 3D window can also be altered by using the zoom tool or mouse scroll wheel with the shift key held down. Similarly, the distance of the camera from the data can be altered by using the zoom tool or mouse scroll wheel with the control key held down.
If 'propagation' is checked then light transport will be modelled for the directional lights (straight on and other light) which causes shadows to be displayed. These shadows are only cast by the side (other, or mobile) light, and are affected by object translucency and colour. If the '+ ambient' checkbox is clicked this will also model propagation of ambient light, including scattering for volume rendering and occlusion for surfaces. Again, only for OpenGL 3.0 or above.
The 'ambient' slider controls how much ambient light there is in the 3D window. Since both secondary scattering and occlusion are calculated from the ambient light, this level also controls how much occlusion and scattering will be visible. The radiant light is decreased proportionally as this value is increased.
The 'scattering' slider enables (if the value is greater than zero) the modelling of ambient scatter (when volume rendering) or ambient occlusion (when showing surfaces). The effect is most easily seen by temporarily increasing the level of ambient light. The extent of scatter or occlusion depends on the slider value. This is also only enabled for OpenGL 3.0 or above.
The 'balance' slider sets the proportion of that radiant light coming from the front or the other (side, or mobile) light. Since shadows (if enabled) only appear from the other light, this also controls the depth of the shadows with respect to ambient light.
The ambient and front 'warmth' sliders control the colour of these lights. Fully left creates a cold, blue-ish light as if viewing at night time. Fully right creates a warm yellow/red light as if viewing by candle-light. The 'white' buttons set these sliders to the mid-point, which gives white light.
Whilst the ambient light has no direction, and the front light is fixed, the other (side, or mobile) light is much more flexible.
The 'rotation', 'position' and 'distance' sliders affect where this light is actually located. The left-right rotation controls the full rotation from front (slider in the centre) to directly from the side (slider half way to either extreme) to behind the data with the light shining towards the viewer (slider either full left or full right). The up-down location adjusts the location from straight down to straight up (when the left-right slider is in the centre) or from top-left to bottom-left (when the left-right slider as half way to the left, and hence the light is shining from the side). The far-near distance controls how close to the data set the light is, with 'far' (slider full right) using a directional light (i.e. a light at infinite distance) and 'near' (slider full left) positioning the light very close to the current centre of the view.
It is also possible to fix this light at a particular location in the data. Just define a landmark anywhere in the data set, and then select that landmark from the 'Fix light at' list. In this case, the 'Distance' slider affects how far the light will penetrate into the data set from the fixed location. Subsequently moving the landmark in any window will automatically move the light location as well.
All the lighting controls affect both the display of surfaces and volume rendering. In the latter case, locating the light behind the data and shining forwards can effectively highlight more transparent sections, and using a point light can draw attention to particular features.
The 'brightness' slider increases the brightness for radiant (not ambient) light only for volume rendering, and only when the surface is being displayed with radiant shadows enabled. This is designed to compensate for the decrease in light levels due to the attenuation of surrounding (but not necessarily visible) regions.
The 'warmth' slider controls the colour of this light, just as for the ambient and front lights. For instance, the ambient and front lights could be set slightly cold, and the other light slightly warm, which would create the effect of being lit by a candle at night.
Lighting settings
Other (mobile) light