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.

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.

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.

This package provides processing pipelines for structural MRI.

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.

This package provides programs to perform EM based segmentation of images in nifti or analyse format.

Nilearn enables approachable and versatile analyses of brain volumes and surfaces. It provides statistical and machine-learning tools, with instructive documentation & open community.

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.

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

This package provides the version schemes used for packaging software from the NiPreps organization.

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.

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

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.

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.

MRtrix3 provides a large suite of tools for image processing, analysis and visualisation, with a focus on the analysis of white matter using diffusion-weighted MRI.

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.

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.

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

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).

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