AutoTract is an automatic tractography tool featuring advanced processing tools (using FiberPostProcess) to clean fiber tracts after the initial tractography (done with the Slicer module TractographyLabelMapSeeding).

This work was supported by the National Institutes of Health (MH064065, MH070890, MH091351, MH091645, HD079124, HD03110).

Find the software on NITRC as well as its tutorial.

• a DTI image on which you want to perform fiber tractography
• a reference DTI atlas + a folder containing the tracts of this atlas (this will serve as label maps for the tractography)
• (optional) a WM mask
• (optional) a CSF mask

• ITK (v4.7 and above) download page
• Qt4 download page
• QTGUI / QTtToCppXml source code
• SlicerExecutionModel source code
• VTK (v6.1.0 and above) download page

• DTI-Reg (requires ANTS, ITKTransformTools, dtiprocess, ResampleDTIlogEuclidean) NITRC page
• ANTS source code
• ITKTransformTools source code
• DTIProcessToolkit (for dtiprocess and fiberprocess) NITRC page
• niral_utilities (for ImageMath, polydatatransform, MaurerDistanceTransform) NITRC page
• ResampleDTIlogEuclidean source code
• Slicer (for TractographyLabelMapSeeding) download page
• DTIFiberTractStatistics (for FiberPostProcess) NITRC page
• unu (part of teem) download page
• python (v2.7.5 and above) download page

AutoTract --noGui --parameters [parameters_config_file.xml] --executables [executables_config_file.xml]

Note: An easy way to generate the basic XML configuration files is to launch AutoTract with the GUI and click File->Save Parameter/Executable Configuration, it will generate the XML file and you can modify the values in that file afterwards.

• Post Processing comparing the shape of the reference tract (by generating an "average" tract? curvature? bounding box?) to further refine the processing
• Tract specific parameters
• Log window with the option of showing details on each tract process
• CMake using Superbuild
• Additional unit and integration tests
• Detection of the end of the pipeline is not managed by the UI (run/stop pushButtons do not change once the pipeline ends)
• State of AutoTract (running/not running) should change the exit message ("Do you want to kill the processes running?")

See LICENSE