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[LOW (or medium?) PRIORITY] Meeting discussion 12/1: Medium priority for alpha testing; and Donna uses.

  • How should a histogram be displayed?
     DVE: 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?
     DVE: 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?

Meeting discussion 12/1: medium priority to include stats from Caret 5 when we have histograms.


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

Meeting discussion 12/1: allow user choice to show comparable locations on both left and right hemispheres (e.g. for connectivity). The other hemisphere be a different color or shape, or a ghosted image. This is low priority.

  • Description of identified nodes in Info box

Meeting discussion 12/1: want it to be easier to see important information. Jenn will lead evaluation of what from Caret 5 should be able to be done. Low-medium priority.


  • How is metadata viewed and edited?

Meeting discussion 12/1: have a follow-up discussion next week


  • 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?
DVE: 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’]

Meeting discussion 12/1: Agreed to keep naming of Tab Montage and Volume Slice Montage

Oblique Volume Slice Viewing

[LOW priority]

  • How should this operate (from user-perspective).
     DVE: Revisit features people like in Caret 5


  • Is Workbench being 'overdesigned'? That is, too many controls/features?
  DVE: IMHO, not yet!! But it’s good to keep asking.
  Meeting discussion 12/1: Good principle to take a hard look at every request. That said, keep Whole Brain view.

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?
   DVE: I like it separate as it currently stands (pop-up). 

Meeting discussion 12/1: Tim L. would like to have basic thresholding more easily available and is generally against pop ups. We will look for broader feedback.

Save and Manage Loaded Files

  • Are controls and functionality sufficient?
  DVE: 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]

Meeting discussion 12/1: Want to be able to remove files in batch, using check-boxes? Group was not sure this would be desirable-- look for additional feedback. Check for modified files when the program exits. No additional actions needed at this time.


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

Meeting discussion 12/1: Do we want a scene exporting functionality (including files)? Yes: can achieve this using spec files-- packaging this more efficiently is LOW 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

Meeting discussion 12/1: Can spec file contents be grouped by anatomy (as a user choice)? MEDIUM priority to implement this. In Spec File Dialog, add a button to open individual files from the dialog box-- MEDIUM priority. Also add a button to pull additional files into the spec--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 mode and the function of the mouse buttons. Is this needed in Workbench?
LOW PRIORITY- we’re tight on space as it stands.

Meeting discussion 12/1: change cursor type to reflect mode. This would help new users. MEDIUM priority-- will add as tools are added.


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

Meeting discussion 12/1: MEDIUM-HIGH priority. Thresholding on p (or q) values is desirable. Metadata should include these statistics-- NIFTI intent files include this. Need to have Matt and Yizheng play with existing datasets in Workbench and see what can be done currently. Question as to whether this raises the priority for histograms.

Thresholding types

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.

 DVE: 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.

Thresholding 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?

DVE: 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?

JE: I think the icons are good for the overall look of the UI, especially when you are first interacting with the program and are looking for some things that are immediately understandable and familiar. I think we could do a medial wall patch on an icon-- we might just have to mark the "M" in gray.

Meeting discussion 12/1: Group agreed the icons add value. Add a gray dot medial wall. Make context-specific (based on Tab).


  • 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?

Meeting discussion 12/1: Button on top does not need to say number of toolbox. On Toolbox, add name, e.g. Cortex Left Toolbox. HIGH priority. Add Toolbox and Toolbar toggle buttons to the right of the Tabs.

User Views

  • Currently, a user-view store only the viewing transformations (pan, zoom, rotate). Nothing more and hence, the name 'view'.

JE: It looks like the user views are currently saved as a preference of Workbench (just like if you change the background color) regardless of whatever spec file you had loaded in or whatever new spec file you load in. That is okay with me, but we need to also have the ability to save favorite views to a file (spec or other).

  • 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.

JE: The window layout status would more appropriately be a preferences option that would by default be kept between sessions. Most users will likely have a preference for window size etc. that they would like to keep when working between projects.

  • Currently User Views don’t work when Yoking is turned on.

Meeting discussion 12/1: Saving favorite views to a file is LOW priority. Developing generic pre-set scenes is a LOW priority.

View Menu

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

DVE: I like it

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?
DVE: user-selectable, stored in user preferences.
  • Are the slices axes characters displayed in single slice view, all slices axes view, montage view, …?
DVE: just in single slice view (at least for starters)

Meeting discussion 12/1: Include in montage view but once per montage, not once per frame.

Slice Index Crosshairs

MEDIUM-LOW priority

  • 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?
DVE: User selectable, stored in preferences
  • Are the volume crosshairs displayed in single slice view, all slices axes view, montage view, …?
DVE: single slice, and all slices
Need to add point and click repositioning of slices in all slice view

Meeting discussion 12/1: want crosshairs across montage view. Want to default montage to axial or coronal view (set in user preferences) not to a black screen. Gray out non-logical choices?

Slice Coordinates

HIGH priority

  • Are the slice coordinate(s) displayed? (X, Y, Z) or just coordinate from viewed axis?
DVE: I vote for x,y,z.

What is displayed in montage?

DVE: Display slice value in corner of each slice.  Provide option to display in mm or slice number (with expected 0.8 mm volume slices, this will be important) 

Preferences or workbench session?

for what?

Meeting discussion 12/1: change to Coordinates and add a coordiante control. Add interpolated volumes as an option in Settings under Layers - LOW priority. To montage add slice coordinates (including on top of zoomed image).


Yoking links the views of models in multiple windows.

Yoking: change spin box to radio buttons - LOW priority. Need to combine some of the group yoking controls - LOW priority. Do we need additional yoking types? Also see Yoking section.

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
DVE:  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.

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.

Ideas from Brain Explorer 2

  • There are a few things that stand out right away in Brain Explorer 2 (Allen Brain Institute visualization program) that we might consider:

1. There are no distinctions between showing structures, volume sections, or both. You just turn on what structures/slices you want to see, much like our whole brain mode.

2. Even when only one plane of volume sections are showing, you can pan, rotate or flip the slice (also available in our whole brain mode)

3. There is a zoom bar slider at the bottom of the viewing window for more obvious zoom capability. Also the mouse wheel can be used for zooming.

4. In selection mode, you can grab a volume plane and pull it through the surface to show different slices (rather than set the volume slice number).

5. Clipping planes can be viewed as a transparent box, and in selection mode, grabbed to cut through a surface.

6. The 3D structures themselves (not just layers) can be displayed as transparent.

7. Clicking on “Find genes” in Brain Explorer 2 opens a default web browser and takes you to the gene search page on the Allen Brain Atlas site. IF you start at the Allen Brain Atlas site you can click on Brain Explorer and a launch application dialog comes up with Brain Explorer 2 as an option. -I particularly like the ability to link between the web search and program from both directions.


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