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.

The purpose of the LPlib is to provide programmers of solvers or automated meshers in the field of scientific computing with an easy, fast and transparent way to parallelize their codes. This library is based on posix standard threads, also known as pthreads, thus taking advantage of multi-core chips and shared memory architectures supported by most platforms (Linux, macOS, Windows).

Version 4 provides an early implementation of colored grains scheduling for better scaling and memory localization with high core count systems.

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.

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.

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.

MRIQC extracts no-reference image quality metrics from structural (T1w and T2w), functional and diffusion MRI data.

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

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

Convert data from DICOM and organise the resulting NIfTI files into BIDS.

Nipype provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages.

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

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

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.

FSL is a comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data. FSLeyes is a GUI for visualizing and editing brain images, from different sources and platforms.

dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format. dcm2niix is also able to generate a BIDS JSON format sidecar which includes relevant information for brain scientists in a vendor agnostic and human readable form.

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 a Pydantic schema for BIDS Stats Models.

ANTs is a C++ library available through the command line that computes high-dimensional mappings to capture the statistics of brain structure and function. It allows one to organize, visualize and statistically explore large biomedical image sets.

TE-dependent analysis (tedana) is a Python library for denoising multi-echo functional MRI data.

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

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.

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

SDCFlows (Susceptibility Distortion Correction workFlows) is a Python library of NiPype-based workflows to preprocess B0 mapping data, estimate the corresponding fieldmap and finally correct for susceptibility distortions. Susceptibility-derived distortions are typically displayed by images acquired with EPI MR schemes.