Options
This page will describe the options listed in the various menus -- mostly the options menu -- and describe their effect. Note that all of the options refer to a single dataset. In the provided images, the sample dataset is selected (see Datasets and view manager)
######Threshold type Specifies whether the threshold is currently proportional or absolute.
######Propotional threshold The current value of a proportional threshold. Only enabled if current threshold type is proportional. A threshold of .95 means that the lower 95% of connections (including zeros) are discarded, and the top 5% are retained.
######Absolute threshold The current value of an absolute threshold. Only enabled if threshold type is absolute. A threshold of .95 means that all connections with value lower than .95 are discarded, and all others are retained.
######Module connection style When viewing a single module, restricts the connections shown on the 3D brain and circle views to only intramodular connections (connections with both ends in the specified module), intermodular connections (connections with exactly one end in the specified module), or both. Has no effect outside of viewing single modules.
######Color on Show the color of the connections scaled to connection strength, or show a monochrome (i.e., binarized) network.
######Colorbar Displays a colorbar showing the mapping of color to connection strength on the 3D brain view.
######Line width Increases the line thickness. This was originally added for the creation of high resolution images, but the resolution is still very bad. I will fix it in the near future.
######Interhemispheric / Left / Right conns on Turns on or off the connections entirely in the left or right hemispheres, or between hemispheres. In order for this to take effect, you will have to reset the display.
######Floating 3D text on Disabling this will turn off the 3D text showing the label name in the 3D brain view.
######Show scalar colorbar
Displays a colorbar on the 3D brain view that shows the mapping of scalar quantities to colors. This colorbar is misleading, though, because in order to display properly these scalars are normalized between
0 and 1. For accurate statistics, multiply by the maximum value of the statistic (which can be found in the statistics panel, you can use the console to find it -- i.e. max(self.controller.ds_instances["dataset_name"].graph_stats["stat_name"]))
######Surface style
Makes some cosmetic adjustments to the way the surface is displayed. Note that cracked glass takes a little while to load (proportional to the number of ROIs) -- it is the glass surface, except with spaces in between regions on the cortical surface.
######Surface opacity Adjusts the opacity of the surface. Low values are recommended. High values between .4 and 1 (except for 1 itself) are generally not at all useful.
######Left / Right Nodes Turns on or off the left hemisphere and right hemisphere nodes in the 3D brain view.
######Left / Right surfaces Turns on or off the left hemisphere and right surfaces in the 3D brain view.
######Circle symmetry Choose the symmetry type displayed on the circle plot. If set to bilateral, the circle will be bilaterally symmetrical, starting at 12 and ending at 6 on both the left and right hemispheres. If set to radial, the circle will be radially symmetrical, so that the left hemisphere displayed on the left half of the circle proceeds forward from 12 to 9 to 6, whereas the right hemisphere proceeds forwards from 6 to 3 to 12.
######Circle rendering At high resolution parcellations, rendering the circle plot can be very slow. When set to disabled, an improvement in performance ensues by simply not rendering the circle plot or creating its underlying data structures. When set to asynchronous, the rendering steps are done in a separate thread so that the user can manipulate other parts of the GUI. Unfortunately at the moment selecting the asynchronous option sometimes causes the program to crash with graphics library errors, because certain operations incorrectly think they need access to windows that are not on the screen to do this rendering. See also (max edges)
Each color map in this section refers to a different color scheme somewhere within the program.
If the value of the colormap is file, a .lut file should be specified. An example .lut file is located at path_to_cvu/cvu/data/cmaps/test.lut. This particular lut file corresponds to the image test.png in the same directory.
You can make your own colormaps with .lut files using the color editor).
To invert a colormap so that the highest values correspond to the low end of the colormap and vice versa, check the reverse button.
The slider between 0.0 and 0.5 is only usable with the heat colormap. With this colormap, extreme values near the end show up in blue or red colors that increase in intensity near the extremes, while colors in the middle are a flat grayish/black color. You can adjust the threshold at which black turns to color with this slider.
######Default colormap This color map is used for node color in the 3D brain view whenever there are no scalars being viewed, and multi-module mode is not active. All nodes receive a value of .3 in this colormap (i.e., they have whatever color is mapped to the value .3), except when viewing single modules, in which case members of the currently selected module have a value of .8.
######Scalar colormap This colormap is used for scalar values on each plot. In the future this may be changed so that different plots can have different colormaps, however this is rather complex to code and there are other features that take priority.
######Conns colormap This colormap is used to display the color of connections in the 3D brain and circle views.
######Matrix colormap This colormap is used to display the color of entries in the matrix view.
This is a list of network statistics that will be calculated when calculating statistics using the stats panel. See Network statistics and modular structure