How do I control the overlay colors?
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Q22. How do I control the overlay colors?
Overlay colors are determined by the "Function" dataset. The threshold slider on the "Define Function" control panel interacts with the threshold data brick from that dataset to determine which voxels will be cut off and not be overlaid in color. You can use the "**" control below the threshold slider to control its range, in powers of 10. If the threshold data brick has statistical parameters attached to it (in the .HEAD file), then the nominal p-value is shown below the threshold slider.
For the fim (etc.) dataset types, the threshold brick is fixed. For the fbuc ("bucket") dataset type, any brick within the dataset can be used as the threshold. If the current "Function" dataset is the bucket type, then a pair of choosers labeled "Func" and "Thr" are activated. The latter lets you pick the threshold brick; the former lets you choose the functional brick.
The colors are computed from the functional brick. The colors of the data that pass the threshold are determined by the color slider to the right of the threshold slider, and by the "range" controls to the far right/bottom. By default, "autoRange" is on, which means that the maximum value in the functional dataset brick is mapped to the top value on the color slider (1.0). By clicking "autoRange" off, you can enter a value in the data field below, and that will be the value mapped to 1.0. For example, if you want to have values of 5.0 mapped to 1.0, you can type "5.0" in that field. Functional values over 5.0 are treated as equivalent to 5.0 in this mapping. If you want to turn those off entirely, you can do so by setting the top color of the color slider to "none" (click in a color panel to change its color value). Then choose the mapping range appropriately to get the colors you want with the remaining part of the color slider.
The number of color steps is chosen by the menu labeled "#" just below the color slider. The toggle switch labeled "Pos?" allows you to change the color slider data range from the default [-1..1] to be [0..1]. This is appropriate if your functional data is always non-negative (or if you just don't want to see the negative functional values). There is no way to display only negative function (unless you just set all the positive colors to "none").
It is also possible to change the upper range of the color slider away from the default value of 1.0. This is done using the Button-3 popup menu attached to the "Inten" label at the top of the slider. This feature, and other facets of the color slider, are more fully described in the file README.setup.
N.B.: It is important to realize that a functional value of zero will never cause a color overlay, even if it is in the range of one of the color slider panes.
[Answer edited 04 Mar 2000]
This FAQ applies to: Any version.
