BrainJ3D

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BrainJ3D
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What is it?

• A tool to visualize the brain. Including
  structural volumes, functional volumes, surfaces,
  veins/arteries and photos.
• Allows mapping of points.
• It is written in Java/Java3D so it is cross
  platform.
• Utilizes Java RMI to provide client/server and
  standalone modes with one code base.

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More

• It will replace
• Brain Mapper
• Visualization Applet
• It will be more maintainable.
• It will reduce dependence on Skandha4.
• It support SPM file types
• We can leverage functionality
• It increases user base.

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Where is it?

• It has most of the functionality of the Brain
  Mapper and the Applet that we want to implement.
• It is not ready to replace them yet.
• It doesnt support saving of data.
• It doesnt generate veins or arteries.

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Architecture
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Client/Server

• Uses Java RMI.
• One server can serve multiple clients.
• Uses the Java3D offscreen option for rendering.
• Uses same code base, so it often works without
  much additional work.

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Milestones

• M1
• Create a workspace that organizes data.
• Show functional activation.
• Fully implements mapping (display, interface,
  loading and saving (not done)).
• Support more file types Matlab 5 (not done), 3D
  formats done.
• Implement a cutaway view.

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Workspace

• Organizes and manages patients data
• XML format, so it is easy to read and edit.
• Categories can be added and removed.
• Names can be changed.

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Workspace

• Future versions will use the workspace to manage
  coordinate systems (space)
• Data should be displayed in a consistent space,
  but it is often imported in different spaces.
• So we can have the workspace transform the data
  as needed.

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Functional Activation

• Functional data can now be overlayed on
  structural data.
• An arbitrary number can be overlayed.
• Transparency is supported.
• Different color schemes can be chosen for each
  functional volume, i.e.. Warm or green or cold.

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Mapping

• You can map points and label the brain
• You can display text and/or a choice of shapes.
• It supports marked nodes.
• You can pick up and move points.
• It supports multiple maps.

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Mapping

• Saving is not yet implemented.
• It only loads the skanda4 file format.
• This doesnt support all the functionality that
  BrainJ3D has.
• So it isnt an ideal format for saving.

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File Formats

• It interfaces to Java3D file loaders, so it
  supports almost all 3D formats to some extent.
• But SPM produces files in Matlab 5 format.
• The specifications for this is huge.
• No file loaders in Java are readily available.
• They are available in C.
• Minc is not supported.

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Cutaway

• You can cutaway the brain and look inside
• It uses the structural volume and a brain mask to
  achieve this.
• You can overlay fMRI onto these structures in the
  same way as the volume viewer.

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Remote mode

• Almost everything works perfectly in
  client/server mode
• the cutaway does not work. A bug in how Im
  using Java3D in offscreen mode.
• Everything else works fine with some expected
  performance loss.
• Security issues need to implement a security
  manager for user level security.

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Next

• Generate surface models of both cortex and
  arteries/veins.
• Probably require dilating the brain mask.
• Fix the user interface.
• Including a help system and meaningful exception
  handling.
• Document code.
• Saving files.

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More

• Level of Detail nodes. We can have two different
  models and then switch them when we need faster
  rendering.
• Have underlying fMRI be visible on the surface
  model by changing the surface color in some
  areas.
• Creating crude brain masks.
• Synchronize interfaces.

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Future Stuff

• Try and utilize the FM
• Im not really sure how, but it could be a good
  resource.
• Connect to the brain map database.
• Interface to the Talarach daemon.

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Where to now?

• Tonga, The Friendly Islands
• 15-23 S 173-177 W
• Only Polynesian Monarchy.
• Never a colonial presense
• Consists of 171 islands 45 are inhabited.

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Islands

• 4 Island groups
• Tongatapu is the business center
• Vavau in the north is a tropical paradise
• Haapai is in the middle.
• Niuas are good for culture.
• New Island 6/1995

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The Friendly Islands

• Dubbed that by Captain Cook.
• The Friendliness was a failed plot to kill him
  and take all his stuff.
• They were the Vikings of the Pacific.