TractographyTRX

TractographyTRX is an ITK remote module that provides native support for the TRX tractography file format. It exposes TRX files as ITK ``DataObject``s with efficient access to streamlines coordinates, scalar data, and named groups.

The implementation is backed by trx-cpp, which is vendored and fetched automatically at configure time.

Why ITK and TRX?

At their core, streamlines are just 3D points. ITK specializes in spatial objects, and their associated transforms and processing. TracrographyTRX brings the highly-efficient TRX format to ITK with very little overhead (see Benchmarks). Transform your streamlines along with your images all in one place!

Contents

• Quick Start
  • Prerequisites
  • Building as an ITK Remote Module
  • Building Standalone
  • Verifying the Installation
  • Hello World
• User Guide
  • The TRX File Format
  • Coordinate Systems
  • Core Classes
  • Lazy Loading
  • AABB Queries
  • Working with Groups
  • DPS and DPV Fields
  • Streaming Writer
  • Example Results
  • Applying Transforms
• Examples
  • Example 1: Reading a TRX File and Inspecting Metadata
  • Example 2: Spatial Query with an Axis-Aligned Bounding Box
  • Example 3: Streaming Writer with DPS and DPV Fields
  • Example 4: Working with Named Groups
• Command-Line Tools
  • trx_info — Inspect a tractogram
  • trx_add_groups — Atlas-based parcellation
  • trx_group_tdi — Track Density Image
  • trx_extract_subset — Extract streamlines
• API Reference
  • itk::TrxStreamlineData
  • itk::TrxStreamWriter
  • itk::TrxFileReader
  • itk::TrxFileWriter
  • itk::TrxGroup
  • itk::TrxParcellationLabeler
  • itk::TrxGroupTdiMapper
• Benchmarks
  • Data
  • Results
  • Build (standalone)
  • Run the benchmarks
  • Plot benchmark results
  • Environment variables
  • Notes on comparison