Fetal and Neonatal Development Imaging

Fetal and Neonatal Development Imaging (FEDI) is a free and open-source software that provides a suite of command-line tools for processing and analyzing fetal and neonatal MRI data.

Key Features

While FEDI is primarily designed for fetal and neonatal MRI, several tools are applicable to general MRI processing. In summary, FEDI provides:

• Gradient and b-vector tools: Rotation of b-vectors, and gradient-scheme conversion.

• Diffusion MRI preprocessing: Denoising, Gibbs artifact removal, and bias-field correction.

• Outlier detection: Identification and weighting of outlier volumes, slices, or voxels.

• Reconstruction: Diffusion signal reconstruction with integrated outlier weighting.

• Motion correction for diffusion MRI: Robust intra- and inter-volume motion correction designed for fetal and neonatal data, but compatible with any population.

• FOD estimation: Fiber-orientation distribution estimation using a pretrained spherical CNN model optimized for neonatal diffusion MRI.

Note

FEDI is under active development, constantly expanding its functionalities.

Getting Started

FEDI runs on GNU/Linux and macOS. The easiest way to install it is via the pre-compiled packages (see the installation section). A Docker image will be available soon.

All FEDI tools share a consistent command-line interface and are executed from a terminal. For help with any tool, type its name followed by --help.

Tip

Basic familiarity with the Unix command line is required to use FEDI effectively.

Table of Contents

Install

• Before You Install
• Installing FEDI

Getting Started

• Fetal and Neonatal MRI Overview

FEDI Modules

• FEDI Command-Line Tools

FEDI Workflows

• HAITCH: Motion Correction
• Fiber Orientation Estimation with sCNN

Developer Section

• Development Team