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UKF TRACTOGRAPHY

About

We present a framework which uses an unscented Kalman filter for performing tractography. At each point on the fiber the most consistent direction is found as a mixture of previous estimates and of the local model.

It is very easy to expand the framework and to implement new fiber representations for it. Currently it is possible to tract fibers using two different 1-, 2-, or 3-tensor methods. Both methods use a mixture of Gaussian tensors. One limits the diffusion ellipsoids to a cylindrical shape (the second and third eigenvalue are assumed to be identical) and the other one uses a full tensor representation.

Authors: Yogesh Rathi ([email protected]), Stefan Lienhard, Yinpeng Li, Martin Styner, Ipek Oguz, Yundi Shi, Christian Baumgartner ([email protected]) Ryan Eckbo

Installation

1. From Source

Checkout from github:

git clone git://github.com/pnlbwh/ukftractography.git

There are 3 ways to build this project from source, as a stand alone superbuild, against a Slicer 4 build, and as a Slicer 4 extension build (which is more of a test than anything).

a) Standalone Superbuild

cd <build-dir>
cmake <path-to-source>
make
make test

b) Build with Slicer4

cd <build-dir>
cmake -DUKFTractography_SUPERBUILD:BOOL=OFF \
  -DSlicer_DIR=<path-to-Slicer4-Superbuild>/Slicer-build <path-to-source>
make
make test

c) Build as Slicer4 extension

  • Manual build (for the developer to test that the extension can be installed successfully)

    mkdir s4ext_build cd s4ext_build ccmake -DUKFTractography_SUPERBUILD:BOOL=OFF
    -DSlicer_DIR=$soft/slicer/Slicer4-Superbuild/Slicer-build
    -DSlicer_EXTENSION_DESCRIPTION_DIR:PATH=$soft/ukftractography/ukf_tractography
    $soft/slicer/Slicer4/Extensions/CMake make

Extension build, test, package and upload using ExperimentalUpload target (https://github.com/Slicer/ExtensionsIndex#extension-build-test-package-and-upload-using-experimentalupload-target):

cd s4ext_build
cd ukf_tractography-build
cmake -DMIDAS_PACKAGE_URL:STRING=http://slicer.kitware.com/midas3 -DMIDAS_PACKAGE_EMAIL:STRING=<EMAIL> -DMIDAS_PACKAGE_API_KEY:STRING=<API KEY> .
make ExperimentalUpload

2. As a Slicer 4 Extension

Navigate to the Slicer Extension Manager and download UKF Tractography to install it as a Slicer 4 module.

Basic Usage

1. As Command Line Module

The executable will be called 'UKFTractography', and can be found in the bin directory of your build folder.

In order to see all options run.

./UKFTractography --help

In the source directory of the project you will find a shell script called 'sample_run.sh' It should give you an idea of what a function call could look like.

2. As Slicer 4 module

Navigate to the Slicer Extension Manager and download UKF Tractography to install it as a Slicer 4 module. There will be 3 modules under Diffusion-->Tractography: UKF Tractography, vtk2mask, and vtkFilter.

Notes

On a Mac, there are rounding errors that affect the accuracy of 2T FW tracts. This explains why the 2T_FW ctest fails.