ooz / BART-ImageDataView

Brain image data viewer which will be incorporated into the BART application.

ObjC/Cocoa view component to display brain image data. Developed to be integrated into the BART application.

Features

• Displays 4D MRT data in axial, sagittal, coronal orientation
• Single slice or multiple slice (grid) view possible
• Overlay support e.g. for functional data
• Colortables can be applied to overlays
• ROIs can be selected

Integration notice

• MainMenu.xib contains just a dummy window to test the view. The actual view is contained in BAImageDataView.xib
• AppDelegate.m can be seen as an example for view integration in the main app.
• Timestep information is not intended to be manipulated by the user. The view controller BAImageDataViewController allows to set the appropriate timestep.

Important classes

• BAImageDataViewController Primary controller:

  • setting of EDDataElements (MRI data)
  • add/set overlays
  • get ROI controller

• BADataElementRenderer Takes care of the EDDataElement --> NSImage conversion. Encapsulates all the orientation, voxel size/gap, row/col vec and other things that have an impact on the final image. Also translates points in the rendered NSImage back to voxels in the original data.

• BAImageSliceSelector Selects the slices to be displayed in the grid view if the grid shows less slices than the original data offers.

• BAImageFilter High level CIFilter with colortable and parameters (e.g. min, max). Used to display colortables as well as the ROI selection.

• BABrainImageView View class displaying the rendered NSImages. Allows composition of multiple layers and is the first to receive mouse events (e.g. for ROI selection)

• ROI/BAROIController Subcontroller for ROIs. ROI selections are stored in BAROISelection objects. Those can be stacked in a hierarchical compositon. The selections can be rendered as a binary map (type: EDDataElement). This allows them to be treated as normal data (e.g. written to disk, displayed in the view)

TODO

• Filter slices without relevant information. Such slice filters should be subclasses of BAImageSliceSelector (low priority)
• Overlay: What happens if background/overlay are not in the same space? (What happens to the slice/orientation selection tools?)

Issues

• It can happen that the CIFilter is not applied correctly. (e.g. blue-red colortable: one color is missing)

ROI

• View has certain dead spot(s) not pushing mouse click events down the responder chain (although mouse events correctly registered by the view class). Possible future fix:

  1. Make (corrected) click point a property of the view class
  2. Let the controller KV observe it
  3. Remove BAImageDataViewController from the responder chain

• Directly after activating an overlay the ROI selected on the current slice isn't displayed (although selection is registered and handled properly on the lower levels). Workaround:

  1. Click on the ROI you want to select, you won't get any visual feedback
  2. Switch slice or orientation or to grid layout
  3. Switch back to the slice/orientation/grid you selected the ROI on. You will now see the ROI selected in (1.)
  4. All following selections work as expected

• If background image and overlay aren't in the same space (should not be!), ROI selection might be 1 or more voxel off the point that was actually clicked.