Compared to Anatomical Volumes
For the most part, functional volumes are simply anatomical volumes drawn with a heat scale color map instead of in grayscale. So, it is a good idea to read the ScubaGuide/ScubaWorkingWithData/ScubaAnatomicalVolumes ScubaAnatomicalVolume section first.
Loading functional volumes from the menu bar is exactly the same as loading anatomical volumes; you don't even declare it as a functional volume until after it is loaded.
You can specify a volume as a functional volume from the command line with the colormap option.
scuba -v anatomical.mgh -v functional.mgh:colormap=heatscale:heatscale=2,4.5,5:visiblemin=2
Use the colormap option to specify the heatscale value. Use the heatscale option set the heatscale threshold paramaters. You can also use the individual heatscalemin, heatscalemid, and heatscalemid options. You may also want to use the visiblemin option to set the minimum visible value to the threshold min value, so that values below the min threshold will be transparent.
To treat an anatomical volume as a functional volume, go to the Layer panel and select the Heat Scale button. Then configure the Heat Scale Min, Mid, and Max paramaters. These three paramters set up a piecewise linear color map. Values at Min are dark red, going to full red at Mid, then to full yellow at Max.
Most likely, you will want to enable info display in the label area for functional values, so make sure to stop by the Views panel and check the Inf checkbox in the row that your functional volume is in.