Lab Software
Contents
Summary of lab and other related software. If you don’t have experience with medical image analysis, check out this page.
ANTs
ANTs is most well known for image registration, but it also includes image segmentation (Atropos), bias correction (N4), cortical thickness calculator (DiReCT), and access to a variety of ITK-based image processing tools via ImageMath. If you don’t have experience with ANTs, read the scripts in the Scripts/ directory, as the usage examples contain the best parameter settings for most cases.
ITK-SNAP
ITK-SNAP is used for display and interactive segmentation of medical images. It also shows overlays and segmentations, among many other features.
ANTsR
ANTsR provides an interface to ANTs from the R programming language. It makes working with medical images in an interactive way much easier and faster.
c3d
c3d, distributed with ITK-SNAP, provides access to a variety of image processing operations.
Pipedream
Pipedream is a system for doing documented, reproducible, standardized analyses of imaging data. It includes easy-to-use utilities for converting DICOMs to Niftis and organizing data.