(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.







                    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.




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

















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)


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.


  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)

When viewing Surfaces:



 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)


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

            Structures pull down menu   

             Surface pull down menu


 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



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.).



When viewing Surface Montage:



  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.


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:



 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)



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.


             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


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


Connectivity Tab (under construction)

Data-Series Tab



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


Vol/Surf Outline Tab

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