AutoTract

AutoTract is an automatic tractography tool featuring advanced processing tools to clean tracts after the initial tractography. It uses the Slicer TractographyLabelMapSeeding, with tracts from a reference DTI atlas as label maps.

The 3 main steps of the tool are:
-Registration between the DTI image that we want to tract and the reference DTI atlas.
-Tractography of the DTI image using the TractographyLabelMapSeeding Slicer module.
-Process of each tract individually to clean and remove any unwanted fiber.

The processing includes (for each tract):
-cutting every fiber ends that are in the gray matter (cutting them until the fiber ends is in the white matter), based on a white matter mask created by the tool.
-ensuring every fiber is not in the CSF (removes them from the tract otherwise)
-several image comparisons with the reference tracts (such as fiber length matching, use of a distance map to ensure that the tract is close to the reference tract, and potentially to be added later on, shape comparison).
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Specifications

Category:Diffusion MR Fiber Tracking
License:Apache License 2.0
Development Status:5 - Production/Stable/Mature
Domain:Computational Neuroscience, MR
Environment:X11 Applications
Intended Audience:End Users
Natural Language:English
Operating System:MacOS, Linux
Programming Language:C++, Python
Supported Data Format:Nrrd
Other Keywords: atlas, automatic, cleaning, diffusion, DTI, fiber, reference, white matter

Associations


Recent Activity

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File Activity

autotract: AutoTract_v1.1 release

AutoTract-Linux64-1.1.tar.gz posted by Jean-Yves Yang on Jun 30, 2015

Document Activity

Main Folder documentation

AutoTract Tutorial (ppt) posted by Jean-Yves Yang on Jun 30, 2015

Document Activity

Main Folder documentation

AutoTract Tutorial (pdf) posted by Jean-Yves Yang on Jun 30, 2015

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help forum

Welcome to Help posted by Jean-Yves Yang on Jun 23, 2015