Crossing Fiber Stipples for higher-order probabilistic tractography

Requirements

• an installed OpenWalnut using the OpenWalnut_1.4 branch (last tested with (git) revision baf70860)
• an OpenGL and OpenCL capable graphics card (the newer the better) with updated drivers
• OpenCL

Required data

• fiber data (binary vtk polydata file ending in .fib) of a probabilistic tractogram started from a single seed voxel

Getting the source

The source code of the module toolbox can be downloaded here:

Crossing Fiber Stipples - zip version

Crossing Fiber Stipples - tgz version

Installation

• make sure OpenWalnut is installed correctly
• unpack the content of the archives to a separate directory
• navigate to the build folder inside the toolbox
• start cmake-gui and choose the "src" directory as source dir (found in the toolbox folder)
• press configure
• if necessary, input the correct paths to your OpenWalnut installation and press configure again
• if necessary, input the correct paths to your OpenCL installation and press configure again
• press generate
• exit cmake-gui and start building via the build system of your choise (usually make)
• start OpenWalnut and add the path to the module's build folder (click the little cogwheel symbol in the "Module" view and choose "configure modules", then choose "Module Paths" tab and add the path there)
• restart OpenWalnut
• you should now find the "SH Fiber Stipples" module when right-clicking the module view and choosing "Add new Module"

How to use

• load fiber data
• connect "Fiber Resampling" to the fiber data and set "# points" to a large value (100+)
• connect "Align Fiber Directions" to the "Fiber Resampling" module
• connect "Calc Diffusion Direction Map" to the aligned fibers
• connect "Calculate Probability Map" to the original fibers
• connect the diffusion directions and probability map to the "SH Fiber Stipples" module
• load a T1 or similar image for reference and view it using "Navigation slices" module

Optional GM and WM outlines can be shown with the "Isolines" module. The module will render the stipples as long as active navigation slices are present. You can use whatever context you want. Additional tracts can be shown by simply repeating the steps for a different set of fibers. Instead of computing the probability map via the module, existing data can be loaded and input to the module as required.