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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Other Keywords:
atlas, automatic, cleaning, diffusion, DTI, fiber, reference, white matter


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