From Van Essen Lab

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[LOW or medium PRIORITY?]

  • How should a histogram be displayed?
     I like caret5 views
  • What controls are needed for the histogram display?
  • How does the histogram display interact with thresholding controls and palette color mapping?
     Slider bars for upper and lower ranges of palette and threshold.  Can one pair of slider bars be used for both? ('Apply to palette' etc)?
  • Subset (percentages, 2% to 98%) display?
  • Descriptive statistics?


  • Allow identification of corresponding node in 'other' structures.


  • How is metadata viewed and edited?


  • The term 'Montage' is used in two different Workbench functionalities, (1) Volume Slice Montage and (2) Tab Montage. Is this confusing? Can one be renamed?

Not confusing to me – I’m ok to stand pat unless someone has an alternative. However, note that the scrollover text for slice montage should say ‘view a montage of parallel slices’ [NOT ‘orthogonal’]

Orthogonal Volume Slice Viewing

[LOW priority?]

  • How should this operate (from user-perspective).
     Not sure what you mean here.


  • Is Workbench being 'overdesigned'? That is, too many controls/features?
  IMHO, not yet!! But it’s good to keep asking.

Palette Colormap Editing

  • Should the editor for palette color mapping be displayed in a dialog separate from the toolbox or should it overlay the toolbox contents until it is closed?
   I like it separate as it currently stands

Save and Manage Loaded Files

  • Are controls and functionality sufficient?
  Generally very good.  
  Newly named files are saved to spec file by default.  That’s ok, at least for now. [but see spec file below]


  • Generic (Data independent). Needed? [LOW priority]
  • Full (Data dependent). [MEDIUM PRIORITY]

Spec File Dialog

  • Is more functionality need on Spec File Dialog? Grouping/showing/hiding file types, structure-related files, structure-independent files, etc.
HIGH PRIORITY: An option to delete file names from spec file.  
MEDIUM:  Grouping a la caret6 is nice.
LOW: option to view metadata from spec file.
  • Is 'Fast Open of Data File' needed?
MEDIUM priority

Status Bar

  • Both Caret5 and Caret6 contained a status bar at the bottom of the main window. The status bar lists the current mouse mouse and the function of the mouse buttons. Is this needed in Workbench?
LOW PRIORITY- we’re tight on space as it stands.


Thresholding is used to inhibit the display of data that does not meet a numerical constraint such as a statistical significance.


Caret5 and Caret6 both have three types of thresholding that emerged as a result of multi-fiducial mapping.

  • Column - These values are stored in the metric file for each column and are the values entered when mapping a volume using the Attributes->Map Volume(s) to Surface(s) Dialog.
  • Avg Area - These values are stored in the metric file for each column and are a result of the values entered when mapping a volume using the Attributes->Map Volume(s) to Surface(s) Dialog and using Multi-Fiducial Mapping (MFM). When mapping using MFM, the volume is mapped onto each of the twelve surfaces and then the average of these twelve mappings is computed and stored in a metric column. For each of the twelve surfaces, a count of the number of nodes exceeding each of the positive and negative thresholds is found and then an average of these counts is deteremined. The MFM metric column is sorted and the Avg Area threshold is set to the value of the node at the "average count" index from the maximum and minimum values.
  • User - These values may be entered by the user and are neither stored in the metric file nor change when the selected metric column is changed.

Show Subthresh Region Green If checked nodes failing a threshold test are shown in a blue-like green for positive values and negative values for an olive-like green for negative values.

It may be desirable to allow several, generic, namable thresholds that users could create as needed.

All thresholds should be stored with their associated maps.

 I consider Avg Area and Show Subthreshold Green LOW PRIORITY.  We will in due course implement MFM using the Conte69 surfaces (or a subset), but this is a ways off.

UI Controls

Users have expressed a desire for control of thresholds using a slider bar. Slide bars have one slider (not two). Note that a slider bar may not provide the needed resolution to 'fine tune' the thresholding. Coupling the slider bar to a spin box may be a solution.



  • For a single surface view, should the LEFT and RIGHT view buttons be replaced with LATERAL and MEDIAL buttons?

If so, what icons should be used for lateral and medial?

YES, replace.  A black medial wall patch might signify Medial, but this may be hard to achieve.  I am not especially enamored of the icons anyway.  Do they really help?


  • How should toolbox be named? Number of tab that is viewed or number of corresponding window?

JE: Since most of what you set in the Toolbox (the layers etc.) applies to the specific tab you are viewing, it makes sense and is less distracting to me for the Toolbox number and tab number that is viewed to match.

  • For the overlay and connectivity controls, what is the maximum number of characters that should be displayed for the name of a file and the name of a map?

User Views

  • Currently, a user-view store only the viewing transformations (pan, zoom, rotate). Nothing more and hence, the name 'view'.
  • Should the views also include window layout status (window size, number of windows, and window placement? This seems out-of-scope for a 'view' and is similar to Caret6's 'Generic Scenes'. Perhaps 'window layout' might be a better term.

View Menu

Is the View Menu properly designed? There were some changes for selection of the view in the window (normal, full screen, montages).

Volume Slice Viewing

Slice Axes characters (L/R, A/P, V/D)

  • Always displayed or user-selectable. If user-selectable, is the setting stored in the user's preferences or just within the current workbench session?
  • Are the slices axes characters displayed in single slice view, all slices axes view, montage view, …?

Slice Index Crosshairs

  • Never displayed, always displayed, or user-selectable. If user-selectable, is the setting stored in the user's preferences or just within the current workbench session?
  • Are the volume crosshairs displayed in single slice view, all slices axes view, montage view, …?

Slice Coordinates

  • Are the slice coordinate(s) displayed? (X, Y, Z) or just coordinate from viewed axis? What is displayed in montage? Preferences or workbench session?


Yoking links the views of models in multiple windows.

Types of Yoking

  • Normal yoking uses the same viewing transformation data in all windows. Thus, when viewing a left surface from a lateral perspective, a yoked right surface is seen from a medial view.
  • Right/Left Lateral/Medial yoking applies an additional transformation so that when viewing a lateral left surface, a yoked right surface is also seen from a lateral view.
  • Are other types of yoking needed?
    • Volume viewing (slice coordinates)
    • Multiple views of a single surface

UI Controls

  • Should the two yoking controls be combined into a single control (group and type in single control)? If other yoking types are added, the user might be able to select a yoking group with incompatible yoking types.
I vote to replace the second pulldown (off, on, on L/R) with 3 radio buttons: Off (the default), On, L/R.  

  • What are good names for the types of yoking?
see above.
I would put other yoking options on a low-priority back burner.  We had talked earlier about a '180 degree' feature that would allow coordinated rotation of medial and lateral views of one hemisphere.  However, I think that may be tricky to implement along multiple axes and wouldn't add much to what we already have.

Ideas from Brain Explorer 2

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