Child pages
  • Connectome Workbench Help Guide

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

  • Features ToolBox gives you the option to attach the Features Toolbox to the Right side of the Viewing Area, Detach it from the Workbench Window (still completely accessible but not connected), or to Hide it all together.  To activate this Toolbox, click 
  • Overlay ToolBox gives you the option to attach the Overlay Toolbox to the Bottom of the Viewing Area, to the Left side of the Viewing Area, Detach it or Hide it.  To activate this toolbox click 
  • Screen also gives you a few options on how to view the entire Workbench application.
    • Normal is the default and what you see when you first open Workbench.
    • Full Screen expands the Workbench application to take up the entire screen.  Both the Toolbar and Toolbox disappear, intentionally, in this mode.
    • Tab Montage shows all active tabs in one window, simultaneously.  You can still rotate, zoom and pan each of the surfaces or volumes in this viewing mode.
    • Tab Montage (Full Screen) combines the functionality of the two modes above.
      • just press ESC to return to the Normal view from any of these other options

                      Image RemovedImage Added 

 

Surface

  • Information ... gives the information/metadata for the surface being viewed at the moment.

...

Information Window

        Image RemovedImage Added         

When you click on a cortical surface or volume, the information of that specific location (brainordinate) is given in this window.

  • Information such as the node number, anatomical coordinate (x,y,z) location, and any of the file data information (connectivity, label, metric data, dense time, etc) that is loaded whether it is being viewed or not at the time.
  • Clear clears the information out of the window giving you a blank info window.
  • Copy becomes active if you highlight information in this window to then copy and paste in another location (text editor or document).
  • RID removes all ID spheres (nodes) from the cortical surface.
  • Contra ID when selected will create a (blue) node at the same location on the opposite hemisphere as where you click (which creates a green node).
    • All of the same types of information are given for the contralateral node in the information window as well.
  • Volume ID
  • Properties brings up a dialog box with symbol (or node) properties (color and size) that you can change.

...

  Overlay Toolbox: turns the Overlay Toolbox on and off.

Image RemovedImage Added  Features Toolbox: turns the Features Toolbox on and off.

...

Yoking: select a yoking group.  This is a way to link multiple tabs so they all are affected by a single manipulation (e.g.: rotation, zooming, border display, etc.).

          Image RemovedImage Added

  • In order to Yoke two tabs, they must both have the same option selected from this menu.  For example, to Yoke tab 1 and tab 2, you need to select A-On Surface in both tabs.
  • If you then want to Yoke two other tabs, separately from tab 1 and 2, then you would choose another (B thru D ) -Onfor surfaces or E thru H for volumes).

 

When viewing Surface Montage:

       Image RemovedImage Added

Orientation

  Lateral/Medial view

...

(User and Reset buttons function the same as described above)

Montage Selection

Image RemovedImage Added

The first column row of pull down menus sets under the column header Left sets the surface selection for the four left hemisphere surfaces (medial and ventral views of both left and right hemispheres) that are default surfaces for the Surface Montage viewlateral and medial views) and in turn the menus under Right do the same for the right hemisphere surfaces.

The second column row of menus set the surface selection for the additional four surfaces that are displayed when the Enable Dual Configuration check box is selected.

(example image of Dual Config showing midthickness surfaces set in the first column row menus and very inflated surface set in the second column row menus)

Image RemovedImage Added


When viewing Volumes:

...

 Montage of slices (multiple slices at a time)

       Image Added

 Oblique view which allows you to rotate a volume to see it in non-standard orientations. (not functioning at this time)

 Resets the volume position to center and default zoom within the window (only if either of these things are manipulated prior).

...

The Features ToolBox provides access to Borders and Foci Attributes and Selection.  You can pull this ToolBox off of the main viewing area and make it float which will make your viewing area bigger.

Image Removed

Image Added


Group allows you to display or manipulate the same borders or foci in multiple windows.  This functions as Yoking does, so each tab you want to be manipulated simultaneously needs be be assigned the same "Group."

Borders: Attributes

Display Borders check box, when selected, turns on the borders from any border file(s) that is currently loaded, making the borders visible on the surface.

...

This menu will show all of the Border Files that are currently loaded and the individual Borders within those files.  Each File can be collapsed by clicking the arrow by the file name check box.  Each Border File or individual border can be turned off by it's own check box.

Foci: Attributes

Image RemovedImage Added

Display Foci check box, when selected, turns on any foci from a foci file(s) that is currently loaded, making the foci visible on the surface.

...

  This button detaches the ToolBox from the main window, allowing you to move the ToolBox to wherever you’d like on your screen. (to reattach the ToolBox to the main window, just double click in the gray title ribbon of the ToolBox)

Layers Tab

         Image RemovedImage Added

    • On check box allows you to toggle layers on and off with the click of the mouse.
      • This way you can load as many Layers as you’d like and switch between them easily for comparison or layer them on top of each other.
    • Settings includes a few items:
      •  provides a dialog box with Threshold, Palette and Histogram settings.
      •  will display a color bar for the given Metric or Connectivity file.  (e.g. )
      •  allows you to change the Opacity of the top Layer in order to see data that you may have loaded beneath it.

...

Connectivity Tab (under construction)


TimeData-Series Tab

      Image RemovedImage Added

    • Yoke check box allows you to yoke two or more Time-Series to one another.  This way you can go to the exact same time point in multiple Time-Series maps.
    •  Graph button activates the Time Course graph that refreshes with each click on the surface.

...

        • Clear Chart clears what is currently viewed in the graph.
        • Reset View resets the graph view to the default settings.
        • History: Keep Last allows you to control how many graphs you see at a time.  Once you click more locations than you indicate to keep, the oldest graph will be deleted to allow for the graph of the newest location to be displayed.
    • AnimateAnimate plays a “movie” of the time series data by clicking the Animate button.
    • TimeFrame allows you to go to a specific time frame point in a series either by entering the time in seconds frame by number or by using the arrows.     
    • File shows the Time-Series files that are loaded.

Vol/Surf Outline Tab

     Image Removed             Image Added (e.g. of volume surface outline showing Myelin map)

...