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README.md

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 (yogesh@bwh.harvard.edu), Stefan Lienhard, Yinpeng Li, Martin Styner, Ipek Oguz, Yundi Shi, Christian Baumgartner (c.f.baumgartner@gmail.com) Ryan Eckbo

For references and further documentation, please see the Slicer module homepage.

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

**To use previous version of unscented Kalman filter rename unscented_kalman_filter_previous.cc to unscented_kalman_filter.cc **

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

b) Build with Slicer4

cd <build-dir>
cmake -DSlicer_DIR=<path-to-Slicer4-Superbuild>/Slicer-build <path-to-source>
make
make test

c) Build via Slicer ExtensionIndex build

Create local extension index following these instructions, containing at least UKFTractography.s4ext and SlicerDMRI.s4ext (required runtime dependency).

Notes:

  • To manually test the UKF Tractography Slicer module, start Slicer using the launcher named SlicerWithSlicerDMRI available in /path/to/SlicerDMRI-build/inner-build directory. This ensure that the SlicerDMRI modules are loaded and that the required MRML diffusion nodes are registered (i.e vtkMRMLFiberBundleNode).

  • It may be helpful to test the exension upload using your API key.

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 is called 'UKFTractography'. It can be found in:

<build-dir>/UKFTractography-build/UKFTractography/bin/

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.

Files dataset_Mask.nrrd and seeds_full_cc.nrrd in Input folder are mask and seed files of subject 100307 in hcp dataset, download the subject's preprocessed diffusion MRI data from https://db.humanconnectome.org/

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.

Several steps in the SuperBuild process download additional git repositories as CMake external projects. By default UKFTractography_USE_GIT_PROTOCOL:BOOL=OFF indicates to use https:// instead of git://. This default should work behind most firewalls (the git protocol uses port 9418: if this is blocked by your firewall the build will fail). If download problems are encountered, please file an issue.

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