Radu Jianu, Çağatay Demiralp, and David H. Laidlaw
We present a visual exploration paradigm that facilitates navigation through white matter tracts in 3D brain models by combining traditional 3D model viewing with lower dimensional representations. For a given set of fiber tracts we create standard stream-tube models along with a 2D embedding and a hierarchical clustering tree. We then link these three representations using both interaction and color obtained by embedding fiber tracts into a perceptually uniform color space. Our results suggest that combining traditional 3D model viewing with lower dimensional representations can ease navigation through the complex fiber tract models, improving exploration of the connectivity in the brain.
Download (application and two demo data sets ~80MB as of August 2010)
Download and unzip
Run NPerspectives.exe. In case of an error stating that "The application is not properly configured" please download and install the "Microsoft Visual C++ 2008 Redistributable Package (x86)" available [here].
Several preset configurations make it easy to load datasets. To access the presets click on "Presets" on the top-left.
First, choose the "Just Brain" preset and set at the bottom of the dialog the path to a tube file. See tubes.txt in the sample data for formatting examples. This will only load the 3D model and will not perform any computations for clustering, coloring and 2D projection but it is a fast way to get started.
Working with the 3D model
first, activate the "Viewers" tab on the top left and select "Brain Viewer" in the list below. This will bring up the toolbox for the 3D model. Activate the "Selections" group.
position the mouse over the actual 3D model. To move the model in the xy plane, press the right mouse button and drag. To move the model along the z axes, rotate the mouse wheel (not holding any mouse button down). To rotate the model press the 'R' key; this will generate a rotation sphere which you can grab by pressing down a mouse button and rotate.
to perform your first selection, press the left mouse button down. This will bring about a selection sphere. You can move the sphere, as you hold the mouse button down, by dragging the mouse around the screen and by using the mouse wheel or up/down keys for the Z direction. Tubes that intersect the sphere will highlighted as you keep the mouse button pressed and selected once you release the button.
you can change the size of the sphere by pressing the "," and "." keys which should be placed below the "<" and ">" keys (making it more intuitive).
there are 4 modes of selection which you can change from a combo in the Brain Viewer toolbox on the left. The default one is "Add": it adds tubes intersecting the sphere to the current selection. "Remove" and "Intersect" are self-explanatory. "SingleShot" clears the current selection every time a new selection is performed.
if a selection was performed you can hide every other tube by pressing the "H" (hidden) key; you can return to the full view by pressing "H" again.
you can save a selection in the toolbox on the left. Once several selections saved you can compose them using the selection modes. Selections can be save to a file for future use with the same model.
example of how to perform a selection: press "clear selection"; place the selection sphere at one end of the cingulum bundle; change selection mode to "Intersect"; place the selection sphere on the other end of the cingulum bundle; save the selection as "cingulum"; clear selection; set selection mode to "Add"; place sphere along the corpus callosum until you get all of it (and probably the cingulum as well); save selection as callosum_cingulum; clear selection; select in the list the callosum_cingulum selection; change mode to "remove" and select the cingulum selection; save selection as callosum.
The "New Brain" preset computes all the data necessary for a cluster analysis and interaction (a tube distance matrix, a clustering, a coloring and a 2D projection) and stores it in directory for future use. However, beware that these computations take a long time for large datasets of around or over 5000 tubes (3-4 hours). For starters you can experiment with the sample datasets found in ./data/ and refer to bullets 7 and 8. For the "New Brain" preset you need to set the path to a tube file and a folder where you wish to cash the results in. Then press "Load" and wait until the "Preset Loaded" message appears - click ok and restart the application.
Load the "Simple Brain Interaction" preset first. This augments the 3D model with two additional features. Once a selection is performed in 3D a quick clustering is dynamically computed and shown on the right. You can navigate in the clustering space by using the mouse wheel to zoom or by holding the right mouse button down and dragging. You can use the nodes in that clustering to refine your selection (you can delete selected hierarchies in the clustering by pressing delete on the keyboard). Second, given a selection in 3D, you can increase or decrease the selection, in terms of similar tubes, by pressing the "w" and "q" keys. Thus, "w" will bring in tubes that are similar to the current selection while "q" will remove tubes from the selection based on the their dissimilarity to the other tubes in the selection.
Restart application and load the "Load all Brain Views" preset. Select the directory previously used in the "New Brain" preset. You can select points in the 2D projection by drawing selection rectangles around points. Tubes can also be selected from the hierarchical clustering view by clicking on any of the nodes. You can press "control" for multiple node selections.
Email firstname.lastname@example.org with any questions, comments requests for new presets etc.