From Van Essen Lab

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Open Items

Ranking of open items (most to least important):

  1. Caret5 style Volume Surface Outline (Done, JWH, 27 Dec 2011) Caret6 style added since better quality).

Looks good, except that line segments extend too far and overlap one another, which doesn't look so great at high mag in highly curved regions. This also occurs in Caret6. Is there an option for reducing the overlap while preserving continuity? (See image in email as illustration of the issue.)

  1. Surface/Volume Identification Interaction (Done, JWH, 28 Dec 2011)

Works well when clicking surface and jumping to volume. Clicking on volume moves the crosshairs now, but reports: "No volume transformation defined in cifti extension" and doesn't show an id node on the nearest surface.

  1. TimeCourse Graph
  2. Borders (with ability to generate labels/metric patches, i.e. values 0,1 from closed borders) [DVE: move up to #4]
  3. Proper Volume Scaling (like Caret5 so volumes always start fitted in the window) [DVE: move to #5]
  4. GUI Improvements (Cursor, Display Control, Info Window, Status Bar, Thresholding, ToolBar Width, Links, Montage Controls, Orientation, Slice Indices/Coords, Surface Options (Whole Brain), Toolbox, Layers, Connectivity)
  5. Yoking (groups and volume) [DVE: agree with Jenn move lower - to #7]
  6. Foci
  7. Scenes
  8. Identification

JE: I agree with Matt's ranking except that I would move Yoking down to 6. and move Volume scaling and UI improvements up.

Not prioritized:

  • Command Line Options (Workbench)
  • Splash Screen


  • Where do controls for the display of border go (Display Control)?
  • Are the numerous pages for controlling the display of borders from Caret5/Caret6 really needed?
  • Are borders displayed in all windows, all tabs, one window, one tab???

Command Line Options (Workbench)

Add options (parameters) for those that launch Workbench from a Terminal window.

  • -spec <spec file> [-nodialogue]
    • Opens a spec file with the open spec file dialogue (or not) with default tabs (i.e. as if you had opened it from within the GUI)
  • -files <file that caret understands> [additional file that caret understands]
    • Opens any number of files that caret understands (i.e. nii.gz, surf.gii, etc)
  • -help
    • Display brief help describing commandline options
  • -scene <scene file> <scene name>
    • Future option for when scenes are implemented

Notes from JWH: (MG: All okay with me)

  • -spec to show spec file in Spec File Dialog.
  • -spec-load to load all files in spec file and skip display of Spec File Dialog.
  • May want options to set the logging level and direct the logging messages to a file.
  • May want OpenGL timing option, -gl-timing.
  • May want options to set the GUI style: -style style-name

Notes from TC: (MG: I would be fine if it could handle whatever was specified without -spec or -files options)

  • Do -spec and -files actually need to be options rather than just specifying the files? (allowing multiple arguments to a single "-files" would complicate parsing, as opposed to all non-option arguments being considered as files) What else would specifying strings that are not options, or arguments to options, mean?

Note from JWH: (MG: I would be fine with autoloading of files without an option)

  • When parsing parameters, one could assume that the first parameter encountered that does not begin with a hyphen is the first file and that any additional parameters are files. (TC - How about just anything that doesn't begin with a hyphen, and doesn't follow an option that requires an argument, is expected to be a file? This matches most command line parsing.)
  • If more that one file listed and if the list contains a spec file, is this an error? My vote is yes. (DLD seconds that vote.)
  • Should files be automatically loaded unless an option is selected in which case the files (or contents of spec file) are shown in the Spec File Dialog (even if there is not a Spec File)? Or, should files be shown in Spec File Dialog unless an option is specified?
  • Thus, "workbench [options...] [file(s)]"

Notes from DLD:

  • Before moving to ubuntu, I used to use -style Cleanlooks in order to navigate lengthy menus (e.g., D/C: Page Selection when many files are loaded). I don't know if other users will miss the -style options.
  • The old -xy option was handy for making movies.

Connectivity Time Series

  • Display timecourse in a graph


  • Change cursor style to represent mouse mode (view, draw border, etc).

Display Control

  • Use for controlling display of borders, foci, volume surface outlines?
  • Displayed with button in tab bar (next to toolbar/toolbox buttons at right side)?


  • Where do controls for the display of foci go? (Display Control)?
  • Are the numerous pages for controlling the display of foci from Caret5/Caret6 really needed?
  • Are foci displayed in all windows, all tabs, one window, one tab???

GUI Bugs

  • If map is in the Palette Editor and the map is deleted, this may result in a crash.


Interhemispheric Identification

  • Allow identification of corresponding node in 'other' structures.
  • How is this controlled? Through Preferences, Display Control, or on Info page of Toolbox.
  • What is color of an interhemispheric identified node symbol?

Info Window

  • Move out of toolbox?
  • If so is it docked; right side of window? Or is a standalone window link in Caret5/Caret6?
  • Displayed with button in tab bar (next to toolbar/toolbox buttons at right side)?

Info Window Contents

  • Format of information?

Surface/Volume Identification Interaction

  • When a surface node is identified, volume crosshairs jump to location.
  • When a voxel is identified, the corresponding node is identified. If there is more than one anatomical surface loaded for a structure, which surface is used? MG: it is necessary to allow the user to pick this. Perhaps a Surface tab is needed in the toolbox that contains this (and eventually other settings from surface miscellaneous).


  • Generic (Data independent). Needed?
  • Full (Data dependent).

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

Splash Screen

Consider a Splash Screen similar to that provided by Xcode (Apple's Software Development Tool).

  • Displayed prior to the Main Window.
  • The left side provide information (links) about Workbench and HCP.
  • The right side lists previously loaded spec files with the last opened spec file selected, and at the top.
  • Open Other launches the file dialog for selection of a Spec File. If a spec file is selected, a Browser Window is displayed and the Spec File Dialog is shown with the contents of the Spec File.
  • Cancel simply displays the Browser Window.
  • Open displays the Main Window with the Spec File selected on the right side of the Splash Screen in the Spec File Dialog.


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?

Task fMRI

For T-fMRI task selection we need a better way to show various task contrasts than just time points in a dense time series. It needs pulldown or rows, not just time points. Or perhaps it should be readable as a file type that has maps. This should be a topic for discussion in January.


  • Retain Mapped and Mapped Area?
  • Allow more than one threshold per map?

JE: This sounds like a good idea if you could save multiple threshold settings kind of like a user view, or as meta data in the metric file

  • Have colorbar range in the viewing window reflect the thresholds
  • Move colorbar toggle to the settings (thresholds) box
  • Need to have ability to apply thresholds to other surfaces, especially for the same kind of metric data in the other hemisphere. Button to apply to all active layers? Could there be a type of "yoking" of settings?

ToolBar Width (shrink width)

The minimum width of the toolbar and the toolbox constrains the minimum width of the browser window.


  • Move button to Tools and create menu with entries (or button with popup) 'Allen Human Brain Atlas' and 'Connectome DB'.

Montage Controls

  • In Caret5/Caret6, the first slice displayed was the selected slice (listed in Slice Indices/Coords) of Workbench ToolBar). Should the selected slice be the slice at the center of the montage? This may be better than starting at (xdim/4, ydim/6, zdim/15).
  • Shrink width of controls by changing labels to "Rows:", "Cols:", "Space:" (or "Skip:")


Reorganize controls so width is reduced.

  • Column 1: L, D, P
  • Column 2: R (M), V, A
  • Column 3: Reset, User Views (User View is two lines; User on top of View)

Slice Indices/Coords

  • Holding down buttons of spin boxes should continuously change value until button is released.
  • Reduce width of coordinate spin boxes and show only one digit to right of decimal.

Surface Options (Whole Brain)

Reorganize controls so width is reduced.

  • Row 1: Surface Type selection combo box.
  • Row 2: 'L' checkbox, 'R' checkbox, Left/Right separation spin box.
  • Row 3: 'C' checkbox, L&R/Cerebellum separation spin box.

Can the separation spin boxes be changed to integers (is sub-millimeter resolution needed?)?


The minimum width of the toolbar and the toolbox constrains the minimum width of the browser window.


  • What is maximum number of characters for File items.
  • What is maximum number of characters for Map items.


  • What is maximum number of characters for 'File'? Just list name and exclude path?

Toolbox "Pop-outs"

A desire has been expressed to be able to move a panel from the toolbox and place the panel into its own window (such as the info panel).

This probably can be done in Qt by removing the panel from the 'tab widget' and then re-parenting the panel into a special dialog. Closing the dialog would move the panel back to the toolbox.== Volume Slice Viewing - Oblique ==

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

Volume Surface Outline

  • Where do the controls for this go?
  • Are they displayed in all windows/tabs or selected windows?


  • Add yoking groups
  • MG: I think volume slice coordinate yoking is a medium priority. Ideally the position of the volume and zoom would also be yoked.

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.


Deferred Items


  • How is metadata viewed and edited?

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


  • 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.
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