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FiberViewer Light Tutorial

This tutorial provides a step-by-step guide to using FiberViewer Light for diffusion and tractography analysis in Slicer across Linux, Mac, and Windows users. It covers launching the application, selecting and saving fiber bundles, applying clustering methods, and visualizing results. Users will learn to manipulate files, generate histograms, and save VTK files effectively. The guide also includes controls for viewing and translating settings for better analysis of fiber distributions. Ideal for researchers and practitioners in neuroimaging.

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FiberViewer Light Tutorial

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  1. FiberViewer LightTutorial Berger Jean-Baptiste jean-baptiste.berger@cpe.fr

  2. Launch from Slicer For Linux and Mac users: Open the modules list Diffusion Tractography FiberViewer Light For Windows users: Go into your Slicer directory (Slicer 4.0.1) then open  lib  Slicer-4.0  cli-modules  Double click on FiberViewerLight.exe

  3. Launch from Slicer For Linux and Mac users: Select your FiberBundle You can select a FiberBundle to save on or create a new one

  4. Getting Started • From GUI : • Select a VTK Input File • Choose the Clustering Method • From Command Line : • ./FiberViewerLight -i input_name -o output_name

  5. Clustering

  6. Length Method • Fiber extremities is Threshold default values • Bars option is the number of bars that will be used on the histogram if none of the fibers were thresholded • Click on Apply Threshold to display the thresholded fiber • Click Next or Undo to go back to the main screen, Next will keep changes

  7. Length Method • Colors go from blue (shortest) to red (longest)

  8. Gravity, Hausdorff and Mean Methods • Same general approach for each method • Algorithm based on gravity, Hausdorff or mean pairwise distance matrix : • Distance between each center of gravity • Maximum of pair wise distances of two fibers • Mean of pair wise distances between two fibers

  9. Gravity, Hausdorff and Mean Methods • Clicking on “Compute Distribution” will generate histogram • There will be (Max – Min)/Step bars from Min to Max • Click on Next to display generated classes with Threshold value parameter

  10. Cluster Selector • Structure of the table : Number of elements of Idthclass and associated color • Click on the number of elements to select class • Click again to deselect a class

  11. Cluster Selector • Click on “Show” to display selected clusters only • “Undo” to go back to the Distribution panel • “Next” to keep changes and go back to main menu

  12. Normalized Cut • Choose the number of cluster which will be the number of classes • Pairwise mean distance based algorithm

  13. Saving your VTK File • When you are done : • Enter a VTK Filename on the main menu • Or • Click on “Save VTK” on the main menu and it will open a browser. • If there is a VTK Filename specified on the main menu, each time you will click on “Save VTK”, it will update the VTK output file

  14. Visualization

  15. Plane Settings • Display a plane by clicking on Plane Option button • Default display : Center of gravity • Change origin and normal settings and update thanks to the corresponding button • Retrieve coordinates by clicking “Get Plan Param” button

  16. Plane Settings • Translate the plan by dragging it • Rotate the plan by dragging the normal arrow

  17. General Visualization Controls • Drag to rotate the view • Shift + Drag to translate the fiber • Ctrl + Drag to rotate on the perpendicular axe to the screen • Right dragging or wheel to zoom in or out

  18. Contributors • Jean-Baptiste Berger : jean-baptiste.berger@cpe.fr • Clement Vachet : cvachet@unc.edu • Martin Styner : martin_styner@ieee.org

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