MrVista preferences


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Since different people may use mrVista slightly differently, a set of preference variables has been implemented to let the user indicate different possible methods of storing and rendering certain types of data. Here is a list of preference variables. These can all be set using the MATLAB setpref command, and the value can be gotten using the getpref command. In each case, they're kept under the 'VISTA' preferences group: e.g., getpref('VISTA', 'defaultROIPath')

[edit] Preference variables in VISTA pereference group

Can someone please type in the three setPref() commands we recommend everyone should use, or at least corresponding to the defaults?

savePrefs: flag indicating whether to save the GUI settings of an Inplane, Volume, or Flat view window when closing them. If 1, will always save when closing. If 0, won't. [Defaults to 0].

defaultAnatomyPath: location of the reference anatomy directory for a subject.

  • The default is:
    setpref('VISTA', 'defaultAnatomyPath', './3DAnatomy');
  • in KGS-lab, we tend to keep things using a local link:

setpref('VISTA', 'defaultAnatomyPath', './3DAnatomy');

defaultROIPath: location, within the anatomy directory, to save ROIs common to the reference anatomy.

  • For KGS-lab: to share ROIs, set this preference to be:

setpref('VISTA', 'defaultROIPath', 'GrayROIs');

extendedGrayFields: when initializing a gray view, there are fields for left and right gray matter nodes and edges. These fields take up a lot of space when loaded, and are redundant with the 'nodes' and 'edges' fields which have the exact same information -- and they aren't needed for a lot (in fact, it's not clear if they're needed at all any longer). If this preference variable is set to 1, will load these extra fields; if 0, will not load them when you open a gray view (although they'll still be saved in Gray/coords.mat.) Default is 1.

verbose: flag to provide lots of feedback or not. If set to 1, will display a number of waitbars / feedback lines; if 0, will keep more silent. Currently used in loading time series for Time Course UI and Multi Voxel UI, but may be used for other purposes.

xHairMethod: When using the Gray/Volume 3-view window, this preference determines how to render the crosshairs when they're turned on. Default is 1: two intersecting lines. If set to 2, will use lines with a gap by the intersection (a la BrainVoyager).

xHairColor: [R G B] color of crosshair lines in Volume 3-view window.


javaOn (old comment): This preference is relevant for MATLAB versions prior to r2007a. Starting with r2007a, MATLAB has removed the user's ability to disable JAVA; if you try, it provides a link to a page where they essentially state that "JAVA works, so you have to use it! If you notice something wrong fill out a bug report." Indeed, most of the quirks from previous versions which you would fix by setting the javaOn preference are fixed. Also, the function mrvJavaFeature is now called in most GUI functions to detect whether the javaOn preference is relevant to the version of MATLAB you are running, and act accordingly.

flag indicating whether the JAVA figures implemented in MATLAB's Java Runtime Environment are working or not. This determines whether certain GUI controls, like popups, behave nicely or not. On Windows (when using the JRE), setting this to 1 works well. On some linux systems, setting it to 1 may cause weird behavior, such as popup menus flickering, so setting it to 0 is recommended. Defaults to 0.

[edit] Mesh Preferences

[edit] mrVista 2 Preferences

mrVista 2 has a set of preferences of its own. These can be set using 'Edit' | 'Preferences' in a mrViewer UI.

GUI_change_directory: if 1, when navigating sessions with the sessionGUI, will automatically change the current working directory in MATLAB correspondingly. Default is 0.

dockFlag: if 1, will always dock uipanels to the parent figure (e.g. in mrViewer). Default is 0. Setting it to 0 doesn't mean panels are never docked; rather, most panels are kept in their own figure, while others are docked.

alphaMethod: when rendering multiple overlays on an anatomy or a mesh, this preference determines how to handle the question of overlap. If two overlays lay on top of each other, the rendering will be the following for different values of alphaMethod:

  1. average two colors: [1 0 0] + [.2 0 1] => [.6 0 .5];
  2. add and saturate: [1 0 0] + [.2 0 1] => [1 0 1];
  3. opaque: [1 0 0] + [.2 0 1] => [.2 0 1]; % the last overlay is 'on top of' the previous one.
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