STIR is an object-oriented framework for tomographic image reconstruction, with an emphasis on iterative reconstruction in PET and SPECT. This package includes the C++ core and Python bindings.

libspatialindex provides spatial indexing utilities, with support for sophisticated spatial queries and interfaces for updating information and customizing the storage management of indices. The library is written in C++, with a C API.

libsupermesh is a Fortran 2008 library to intersect two overlapping meshes element by element. Pairs of overlapping elements are identified and a local mesh of their intersection is generated.

MVAPICH (pronounced as “em-vah-pich”) is an open-source MPI software to exploit the novel features and mechanisms of high-performance networking technologies (InfiniBand, iWARP, RDMA over Converged Enhanced Ethernet (RoCE v1 and v2), Slingshot 10, and Rockport Networks) and deliver best performance and scalability to MPI applications. MVAPICH 4.1 has support for the Cray Slingshot 11, Cornelis OPX, and Intel PSM3 interconnects through the OFI libfabric library, and for the UCX communication library.

Umpire is a resource management library that allows the discovery, provision, and management of memory on machines with multiple memory devices like NUMA and GPUs.

This package contains the binary resulting from the compilation of hello_c.c in the examples subdirectory of the Open MPI source code. It can be used to check MPI connectivity on a machine/cluster.

MVAPICH2 (pronounced as “em-vah-pich 2”) is an open-source MPI software to exploit the novel features and mechanisms of high-performance networking technologies (InfiniBand, iWARP, RDMA over Converged Enhanced Ethernet (RoCE v1 and v2), Slingshot 10, and Rockport Networks) and deliver best performance and scalability to MPI applications.

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

pybids provides a set of tools for working with BIDS datasets. The BIDS standard aims at organizing and describing neuroimaging data in a uniform way in order to facilitate data sharing within the scientific community.

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.

Surfa is a collection of Python utilities for medical image analysis and mesh-based surface processing. It provides tools that operate on 3D image arrays and triangular meshes with consideration of their representation in a world (or scanner) coordinate system. While broad in scope, surfa is developed with particular emphasis on neuroimaging applications.

migas (mee-gahs) is a Python client to facilitate communication with a migas server.

NeuroImaging Workflows provides processing tools for magnetic resonance images of the brain.

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.

It helps developers working in continuous integration (CI) environments by providing essential information about the CI server. It can determine if the code is running on a CI server,identify the specific server,and detect if a pull request is being tested.

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.

heudiconv is a flexible DICOM converter for organizing brain imaging data into structured directory layouts.

CiftiLib is a C++ library for CIFTI-2 file reading/writing. It additionally supports CIFTI-1 files, and supports both on-disk and in-memory access. It also provides C++ code for reading and writing generic NIfTI-1 and NIfTI-2 files.

CIFTI (Connectivity Informatics Technology Initiative) standardizes file formats for the storage of connectivity data. These formats are developed by the Human Connectome Project and other interested parties.

See http://www.nitrc.org/projects/cifti/ for more information.

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.

Nifti_clib is a set of I/O libraries for reading and writing files in the nifti-1, nifti-2, and (to some degree) cifti file formats. These are binary file formats for storing medical image data, e.g. MRI and fMRI brain images.

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

DIPY is the paragon 3D/4D+ medical imaging library in Python. It contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.

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

The etelemetry Python client facilitates communication with the etelemetry server, providing version information and checking for critical bugs in projects. The client allows you to retrieve project details and compare versions to identify and warn about problematic versions.