AFNI, Analysis of Functional NeuroImages is a suite of programs for looking at and analyzing MRI brain images at all stages of analysis (planning, setting up acquisition, preprocessing, analysis, quality control and statistical analysis).

NiBabies is an open-source software pipeline designed to process anatomical and functional magnetic resonance imaging data, designed and optimized for human infants between 0-2 years old.

Gifticlib is a a library for reading and writing files in GIfTI format. GIfTI is a standard for Geometry Data Format for Exchange of Surface-Based Brain Mapping Data.

This package provides an implementation of TRX, a tractography file format designed to facilitate dataset exchange, interoperability, and state-of-the-art analyses, acting as a community-driven replacement for the myriad existing file formats.

The fslpy package is a collection of utilities and data abstractions used within FSL and by FSLeyes.

This package provides the Python Client code for accessing neuroimaging templates hosted using TemplateFlow.

The indexed_gzip project is a Python extension which aims to provide a drop-in replacement for the built-in Python gzip.GzipFile class, the IndexedGzipFile. indexed_gzip was written to allow fast random access of compressed NIFTI image files (for which GZIP is the de-facto compression standard), but will work with any GZIP file.

NIPY provides a platform-independent Python environment for the analysis of functional brain imaging data.

fMRIPrep is a fMRI data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting. It performs basic processing steps (coregistration, normalization, unwarping, noise component extraction, segmentation, skull-stripping, etc.) providing outputs that can be easily submitted to a variety of group level analyses, including task-based or resting-state fMRI, graph theory measures, and surface or volume-based statistics.

This package provides DICOM to NIfTI conversion with the added ability to extract and summarize meta data from the source DICOM files. The meta data can be injected it into a NIfTI header extension or written out as a JSON formatted text file.

This package provides programs to perform rigid, affine and non-linear registration of 2D and 3D images stored as NIfTI or Analyze formats.

The fsleyes-widgets package contains a collection of GUI widgets and utilities, based on wxPython, which are used by fsleyes-props and FSLeyes.

fsleyes_props is a framework for event-driven programming using Python descriptors, similar in functionality to, and influenced by Enthought Traits.

The BIDS Validator is a web application, command-line utility, and Javascript/Typescript library for assessing compliance with the BIDS standard.

This package provides utilities for feature analysis, preprocessing and visualization of image quality metrics generated by MRIQC.

This package provides Python tools for working with the BIDS schema.

A Python implementation of the moving average principal components analysis methods for functional MRI data translated from the MATLAB-based GIFT package.

Convert3d is a command-line tool for converting 3D images between common file formats. The tool also includes a growing list of commands for image manipulation, such as thresholding and resampling. The tool can also be used to obtain information about image files.

Connectome Workbench is a visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project. It allows exploration of data and activity on the surface, as well as in the volume of the brain.

Nitime contains a core of numerical algorithms for time-series analysis both in the time and spectral domains, a set of container objects to represent time-series, and auxiliary objects that expose a high level interface to the numerical machinery and make common analysis tasks easy to express with compact and semantically clear code.

This package provides a fast implementation of the Levenshtein distance with C++ and Cython.

This package provides tools for unsupervised and semi-supervised morphological segmentation.

WORLD Vocoder is a fast and high-quality vocoder which parameterizes speech into three components:

• f0: Pitch contour

• sp: Harmonic spectral envelope

• ap: Aperiodic spectral envelope

It can also (re)synthesize speech using these features.

This package provides Python bindings for the simstring text similarity matching library.