AutoSeg

AutoSeg is a novel C++ based application developped at UNC-Chapel Hill that performs automatic brain tissue classification and structural segmentation.

AutoSeg is designed for use with human and non-human primate pediatric, adolescent and adult data.

AutoSeg uses a BatchMake pipeline script that includes the main steps of the framework entailing N4 bias field correction, rigid registration to a common coordinate image, tissue segmentation, skull-stripping, intensity rescaling, atlas-based registration, subcortical segmentation and lobar parcellation, regional cortical thickness and intensity statistics. AutoSeg allows efficient batch processing and grid computing to process large datasets and provides quality control visualizations via Slicer3 MRML scenes.
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Specifications

Category:Expectation Minimization, Labeling, Volumetric Analysis, Image-to-Image, Image-to-Template, Spline Interpolation, Nonlinear Warp, Workflow
License:BSD License
Development Status:6 - Mature
Domain:MR
Environment:Win32 (MS Windows), X11 Applications
Intended Audience:Developers, End Users
Natural Language:English
Operating System:MacOS, Windows, Linux
Programming Language:C++
Supported Data Format:ANALYZE, Nrrd, Other Format

Recent Activity

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Tracker Activity

Bugs tracker

Volumetric calculation using ImageStat  posted by Yundi Shi on Mar 26

Tracker Activity

Bugs tracker

Bug when T1 and T2 in different directories posted by Yundi Shi on Mar 24

Document Activity

Main Folder documentation

Sample Computation and Parameters files posted by Jiahui Wang on Dec 28, 2013

Document Activity

Main Folder documentation

Sample Segmentation Results  posted by Jiahui Wang on Oct 31, 2013

Tracker Activity

Bugs tracker

AutoSeg3.0.0c problem in automatic selecting data posted by Yundi Shi on Oct 31, 2013

Tracker Activity

Bugs tracker

ImageMath command not working with AutoSeg_2.9 posted by Jiahui Wang on Sep 12, 2013

Tracker Activity

Bugs tracker

ImageMath command not working with AutoSeg_2.9 posted by David Grayson on Aug 6, 2013

Tracker Activity

Feature Requests tracker

Take "manual mask" for T1 and T2 as input posted by Yundi Shi on Jul 18, 2013

Tracker Activity

Bugs tracker

AutoSeg_3.0.0a not writing the process folder and Data directory into the parameter file posted by Yundi Shi on Jul 18, 2013

Tracker Activity

Bugs tracker

N4 correction does not wok posted by Jiahui Wang on Feb 21, 2013