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 (a work in progress)Connectome Workbench Help Guide

18 May 2012

 

This document is intended to be an informational guide as to what is what in the Connectome Workbench.  There is also a working tutorial available here (Workbench Tutorial) if you are wanting more guidance on how to use the Workbench in all of it’s glory.

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

MENUS

  

Workbench

     Preferences:

                

  • Background Color is where you can set the background color of the Viewing Area.
  • Foreground Color is the color of things such as text labeling volume slice axis and text shown above palette color bars.
  • Data File Open/Save ...
    • On will automatically add files that you open or save to the current Spec file.
    • Off will not automatically add these files to the Spec file.
  • Logging Level lets you set the level of logging information collected; from nothing to the finest of detailed tracing
  • Show Splash Screen at Startup
    • On will show you the Splash Screen with a list of Recently Opened Spec files listed (if applicable).  

                     

                    You can either open a Spec from this listing or use the Open Other ... button to open a Spec file from any location.  The Skip button allows you to skip selecting any Spec file at this step.

                    This splash screen also gives a link to the HCP website and Twitter page.

    • Off will eliminate the Splash Screen from displaying at the startup of Workbench.
  • TimeCourse Animation Starts at allows you to set the Dense Time Series animation start time at either 0.00 or 1.00 (or anytime thereafter).
  • Volume Axes Crosshairs allows you to select if you want to see the axes crosshairs when viewing volume images.
  • Volume Axes Labels allows you to select if you want to see the axes/orientation labels when viewing volume images.

File

  • 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.  If you are opening a file into an existing Spec file, you have the option to Add it to the Spec or not by selecting or deselecting the checkbox at the bottom of the dialog box.

              

  • Open Location allows you to open any Workbench type file that is located on the internet that is accessible via a URL.  Must have a login.

              

  • 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)

              

  • Open File via Spec File opens a spec file window that looks similar to the original data file listing when you first open a spec file.  This gives you easy access to opening files that are already in your spec file.  By deselecting the Auto Close check box, in the bottom right hand corner, this list will remain open which is helpful when you are opening several files at a time.

              

  • Save/Manage Files is the place to save any changes you’ve made to any file, edit the metadata associated with any file, remove a file from your spec file, remove maps, or change a file name.

              

  • Close Spec File keeps Workbench open but will close out all of the data that was opened.
  • Capture Image allows you to capture and save images within Workbench.  You can select the Source, Size, Cropping Options and Destination of the image.

                         

  • Close Tab will close the active tab, which can also be done by clicking on the X that is on the tab itself.
  • Close Window will close the active window. If there is only one window open, this will close the Workbench application altogether.

 

View

  • Toolbar turns the toolbar on when checked and off when not checked.  This is the same function as selecting or deselecting the  button in the upper right hand corner of the toolbar.
  • 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

                       

 

Surface

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

                   

  • Volume Interaction ... unclear at the moment

             

Volume

...

Connect

  • Gives you quick access to both the Allen Brain Institute Database as well as the Human Connectome Project Database (work in progress)

Window

  • Next Tab makes the tab to the right of your currently active tab the new active tab.
  • Previous Tab makes the tab to the left of your currently active tab the new active tab.
  • Rename Selected Tab allows you to change the name of the selected tab to anything you want.
  • Move All Tabs in Current Window to New Windows does exactly what it says, creating as many windows as you have tabs (5 tabs turn into 5 windows).
  • Move All Tabs From All Windows Into Selected Window again, means what it says and your selected window is the active window at the time this option is chosen.
  • Move Selected Tab to Window will give you the option to move your active tab to a window of its own (New Window) or to another existing widow other than the main if you have more than one window open.
    • If you have a tab in another window and want to put it back into the main window you can select this menu option again and select Connectome Workbench 1, just make sure the tab you want to move is your currently active tab.
  • Information Window brings up the information window which displays information about locations identified by clicking on the surface or volume.
  • Bring All To Front is useful when you have multiple Workbench windows open along with other applications.  Sometimes windows can get lost under other applications so this will bring all windows to the front of all other applications.

Help

This menu selection gives you easy access to the HCP website and also to helpful information online 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)

Icons in the upper right hand corner are for quick access to pop-up boxes and menus

  Information: when this button is ON, the Information Window is automatically displayed when an identification operation (mouse click on the surface or volume) is performed.

Information Window

                 

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.

              

  Toolbar: turns the toolbar on and off.

  Overlay Toolbox: turns the Overlay Toolbox on and off.

  Features Toolbox: turns the Features Toolbox on and off.

View (these options are the same in all four Toolbar types)

  • Surface radio button changes the active window to a 3D surface view
  • Surface Montage radio button changes the active window to a combination of left and right hemisphere surfaces with both lateral and medial views.
  • Volume radio button changes the active window to a volume view
  • Whole Brain radio button changes the active window to a combination of all 3D surface views along with all 3 axis of the volume view

When viewing Surfaces:

            

Orientation

 Lateral view of a single hemisphere (or Left hem lateral when viewing Whole Brain)

 Medial view of a single hemisphere (or R which is for Right lateral when viewing Whole Brain)

 Dorsal view

 Ventral view

 Anterior view

 Posterior view

 This is where you can set, name and save your preferred orientation so you can get to it in a click of a button.

 This button will reset your surface back to the default settings (size, location on the screen and lateral view)

Selection

This is where you set the brain structure and the selected structure’s surface

            Structures pull down menu   

             Surface pull down menu

Tools

 Border button opens a menu of options to draw and edit borders. 

 Viewing is the default mouse mode and allows you to perform viewing operations with the mouse

        

Window

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.).

          

  • 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-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 for surfaces or E thru H for volumes).

 

When viewing Surface Montage:

       

Orientation

  Lateral/Medial view

  Dorsal/Ventral view

  Anterior/Posterior view

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

Montage Selection


The first row of pull down menus under the column header Left sets the surface selection for the left hemisphere surfaces (lateral and medial views) and in turn the menus under Right do the same for the right hemisphere surfaces.

The second 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 row menus and very inflated surface set in the second row menus)


When viewing Volumes:

       

 

Slice Plane

 Parasagittal slice view

 Coronal slice view

 Axial slice view

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

 Single slice at a time

 Montage of slices (multiple slices at a time)

       

 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).

Slice Indices/Coords

1st box controls the slice number and the 2nd box controls the coordinate number.     

           

These numbers can be changed by manually entering specific slices or coordinates in each box, by using the up and down arrows next to the boxes or by using your scroll bar with the cursor inside of a specific box.

  • P: controls the parasagittal numbers
  • C: controls the coronal numbers
  • A: controls the axial numbers
  • Origin resets all three slice planes to default settings of slices 127, 147, 127 and coordinates 0.0, 0.0, 0.0

Montage

This is where you set how many Rows and Columns you want to see in your montage and then the spacing (Step) between each slice viewed.

 

When viewing Whole Brain:

         

Orientation

 Left hemisphere lateral view or view from left perspective

 Right hemisphere lateral view or view from right perspective

All of the other buttons in this section are the same as for a single surface view.

 

Surface Viewing

 Surface selection pull-down menu, changes all surfaces being viewed with one selection.

 These check boxes toggle on/off the Left and Right cortex and the Cerebellum (when available) surfaces.

 These controls are to set the separation between the left and right hemisphere structures (top control) and the cerebellum (bottom control)

 (Slice Indices/Coords,Tools and Window sections are the same as above)

 

Anchor
FeaturesToolbox
FeaturesToolbox
FEATURES TOOLBOX

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.



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.

Contralateral check box, when selected, displays borders from one hemisphere on both hemispheres.  This is a way to compare differences between left and right hemisphere borders.

Draw As allows you to change the presentation of the borders being displayed.

      

Line Width and Point Size change the size of the borders lines and points.

Borders: Selection

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


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.

Contralateral check box, when selected, displays foci from one hemisphere on both hemispheres.  

Paste Onto Surface pulls all the foci from their relative space to directly on the surface. why?

Coloring can be set to Focus Name (must click on a Focus to get the name) or to Class Name.

Draw As menu allows you to change the shape of the foci to Spheres or Squares, currently. (other shapes available in the future)

Size changes the size of the foci being displayed.

Foci: Selection

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


Anchor
OverlayToolbox
OverlayToolbox
OVERLAY TOOLBOX 

             ToolBox attached to Bottom             ToolBox attached to Left

 This button closes the Overlay ToolBox  (to reopen the Overlay ToolBox, you can either click on the Overlay ToolBox icon  in the upper right hand corner of the Toolbar or select Overlay ToolBox from the View pull-down menu)

  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

         

    • 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.

                                      (image shows layer 1: Label Composite Parcellation at Opacity 0.60 with layer 2: Metric Myelin map)

    • File pull down menu will show you a list of all of the available files that are currently loaded that correspond to the View (surface, volume or whole brain) in the active tab.
    • Map pull down menu gives you a list of the available map files that are currently loaded for the file you selected from the File menu.
    • Number of Overlays allows you to add layers to the list.  (can't have fewer than 3 layers at any time)

 

Connectivity Tab (under construction)


Data-Series Tab

      

    • 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.

                                        

        • Time(seconds) gives you control to only see the graph between two specific time points.
        • Activity gives you control to only see the graph between two specific y axis measurements.
        • Line Width allows you to change the thickness of the graph line.
        • Autofit Time Lines keeps the graph within the graph window.
        • Zoom X Axis allows you to zoom in in terms of the x axis.
        • Zoom Y Axis allows you to zoom in in terms of the y axis.
        • Show Average will show you the average of up to 5 graphs of time points selected.

                                         (here the blue line is the average of the red and green lines)

                                              

        • 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.
    • Animate plays a “movie” of the time series data by clicking the Animate button.
    • Frame allows you to go to a specific frame point in a series either by entering the frame by number or by using the arrows.     
    • File shows the Time-Series files that are loaded.

Vol/Surf Outline Tab

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

    • On turns that Volume Surface Outline on.
    • Color Source lets you choose what color you want the surface outline to be ... it can be a number of solid colors (from the pull down list) or it can be the color of what is the top layer in any given Workbench Tab.
    • Thickness allows you to make the outline as thick or thin as you wish.
    • File allows you to choose the outline of either the Left or Right hemisphere Midthickness surface.