Software

ITK-SNAP

ITK-SNAP (http://itksnap.org) is a tool for interactive segmentation and labeling of anatomical regions in structural MRI data. ITK-SNAP is a mature software application with a highly functional, user-friendly interface. Its intended audience includes clinicians and biomedical researchers. ITK-SNAP provides semi-automatic segmentation using active contour methods (Zhu and Yuille, 1996; Caselles, 1997), as well as several tools for manual delineation, and highly dynamic image navigation. In addition to these core functions, ITK-SNAP provides a number of supporting utilities. Some of the core features include linked cursor for seamless 3D navigation; manual segmentation in three orthogonal planes at once; friendly user interface for selecting active contour segmentation parameters; support for many different 3D image formats, including NIfTI and DICOM; support for concurrent, linked viewing and segmentation of multiple images; support for color images (e.g., diffusion tensor maps) and statistical overlays; 3D tools for fast post-processing of segmentation results; and an extensive and evolving online tutorial and Wiki. ITK-SNAP is an open-source multi-platform application written in C++, and it takes advantage of the NLM Insight Toolkit (Yoo, 2005). Continued development and maintenance of ITK-SNAP is supported by the NIBIB and the NIH Blueprint for Neuroscience through grant 1 R03 EB008200-01.

ANTS

ANTS is a well-evaluated normalization and neuroanatomy toolkit that enables a wide variety of transformation models, similarity metrics and images to guide brain (or other image) mapping. Particular features are symmetric diffeomorphic mapping, label-guided mapping and tools for estimating surface curvature from images and cortical thickness. Image difference, mutual information and correlation are both available to guide the registration and may be combined in a multivariate way for optimizing complex registration problems.

DTI ToolKit (DTI-TK)

DTI-TK is a spatial normalization and atlas construction toolkit, designed from ground up to support the manipulation of diffusion-tensor images with special cares taken to respect the tensorial nature of the data. It implements a state-of-the-art registration algorithm that drives the alignment of white matter tracts by matching the orientation of the underlying fiber bundle at each voxel, information available uniquely to diffusion-tensor images. The algorithm has been shown to both improve white matter tract alignment and to enhance the power of staistical inference in clinical settings.

DTI preprocessing pipeline

This pipeline has been designed and implemented to support the preprocessing of raw DTI data (i.e., in DICOM format) acquired on the Siemens Trio scanner HUP6. The pipeline software and documentations is available for download from here.

Convert3D

Convert3d (http://itksnap.org/c3d) is a command-line tool that offers complimentary features to ITK-SNAP and is used extensively in our image analysis pipelines. Originally developed for converting 3D images between common file formats, the tool now includes a growing list of commands for image manipulation, such as thresholding and resampling. The distinguishing property of Convert3D is the use of reverse polish notation on the command line, which makes it easy to string atomic commands into fairly complex command-line programs, with no need to save intermediate images.

Hippocampal Subfield Segmentation Protocol

This protocol, developed by John Pluta and Susanne Mueller, is used to generate accurate delineations of hippocampal formation subfields in T2-weighted MRI data.