Documentation/4.3/Modules/TractographyDisplay

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Introduction and Acknowledgements

This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the NA-MIC website. Author: Isaiah Norton, Goldby Lab Author: Demian Wassermann, SPL Contributor1: Steve Pieper, Isomics Inc. Contributor2: Alex YarmarKovich, Isomics Inc. Contact: Demian Wassermann, <email>demian@bwh.harvard.edu</email>

Surgical Planning Laboratory

Module Description

Allows the user to manipulate several different characteristics of the traced white matter tracts. Examples are: change of color; display of the fractional anisotropy along the tract; display of the tracts as tubes or lines; interactive selection of the tracts; and cropping.

Use Cases

Most frequently used for these scenarios:

• Use Case 1: Change the scalar quantity displayed along the tract, like Fractional Anisotropy or Color By Orientation
• Use Case 2: Display the tracts as lines or tubes
• Use Case 3: Interactive selection or cropping of a certain bundle.
• Use Case 4: Interactive editing (selecting/deleting) or cropping of a certain bundle.

Tutorials

Links to tutorials that use this module

Panels and their use

Simple Fiber Bundle Display Control panel Solid Tube Color: toggles on/off solid color for tubes Name: click to make a fiber bundle active Lines: Display the tracts as lines Tubes: Display the tracts as tubes Tubes Slices: Show the tracts intersection with slice planes in the 2D views Glyphs: Display glyphs representing the diffusion tensors along the tracts Tubes Color: Select solid color for tubes Percentage of Fibers Shown: Select how many of the total tracts in the bundle are shown. Useful for performance. Fiber Bundle Selection: Perform interactive selection and cropping of the tracts ROI for Fiber Selection: Select a ROI to use as an interactor with the tracts Disable/Positive/Negative ROI: Set the selection mode to Select everything; Select the tracts traversing the ROI; Select the tracts not traversing the ROI Interactive ROI: toggles on/off the interactive updates during manipulating the ROI ROI Visibility: toggles on/off the selected ROI's visibility Extract Bundle From ROI: Create a new fiber bundle which contains only the selected ones Update Bundle From ROI: Update the current fiber bundle leaving only the selected ones Enable Interactive Edit: Enables individual fiber selection/deletion. First click in 3D view to focus, then use: 's' to toggle selecting/unselecting of the individual fiber under the mouse 'd' for deleting all selected fibers or of the individual fiber under the mouse 'x' for unselecting all selected fibers Advance Display: For the lines, tubes and glyphs Visibility: Toggle the visibility of the bundle Opacity: Change the transparency level of the bundle Color By: Change the way the bundle is colored; either by a tensor-derived property or by a group id Solid Color: Color the bundle of a single solid color References Publications related to this module go here. Links to pdfs would be useful. For extensions: link to the source code repository and additional documentation Information for Developers