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  • Connectome Workbench Help Guide

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Here we begin with our “what is what” guide in the upper left hand corner of the Workbench Window.

MENUS

  

Workbench

     Preferences:

  • Colors tab is where you can set the foreground and background colors for your machine.
  • Logging tab lets you set the level of logging information collected; from nothing to the finest of detailed tracing.
  • Volume tab is where you select if you want to see the axes crosshairs and/or orientation labels when viewing volume images.
  • TimeCourse tab allows you to set the Dense Time Series animation start time at either 0.00 or 1.00 (or anytime thereafter).

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  • New Window opens a new window that ~matches window 1 (same number of tabs with similar visualization in each).
  • New Tab will open a new tab in the active window (in case you have more than one window open)
  • Open File lets you open any file type from any file folder.

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  • Open Recent Spec File gives you a list of your recently opened spec files and the opportunity to easily select one from the list.

              (A Spec file is a list of files that are concurrently loaded)

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  • 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

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This menu selection gives you easy access to helpful information about Connectome Workbench and how to use it. (like this document for example)

 

Anchor
Toolbar
Toolbar
TOOLBAR    (the bar at the top of the viewing window)

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 Database button connects directly to the Connectome Database.  You will need to login to the Database to get further than the home screen.

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 Will show all 3 slice views (described above) in one window

 Single slice at a time

 Montage of slices (multiple slices at a time)

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  • 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 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) -On.

 

Anchor
Toolbox
Toolbox
TOOLBOX (the box at the bottom of the viewing window)

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

  • Information such as the node number, anatomical coordinate (x,y,z) location, and any of the file data information (connectivity, label, metric data, 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 to 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.

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    • Selector check box indicates which connectivity maps are being refreshed at each click of the surface.
      • If you have many connectivity files loaded, this check box will become more important because it will take more time for the data to be retrieved if there are many files checked on.
    • File shows the connectivity file that is loaded.
    • File Type will automatically update to classify what kind of file is loaded be it a Dense Time Series or a Dense Connectome, etc.
    • Graph is only active when a Time Series file is loaded.  When this box is checked and you click the surface showing Dense Time Series data, you will get a pop-up window giving you additional data.

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