FFCx is a compiler for finite element variational forms.

From a high-level description of the form in the UFL, it generates efficient low-level C code that can be used to assemble the corresponding discrete operator (tensor). In particular, a bilinear form may be assembled into a matrix and a linear form may be assembled into a vector.

This package provides the UFCx interface header.

Grace is a 2D plotting tool for the X Window System. It has a Motif-based GUI and a scripting language that includes curve fitting, analysis, and export capabilities.

The Basic Linear Algebra Subprograms (BLAS) have been around for many decades and serve as the de facto standard for performance-portable and numerically robust implementation of essential linear algebra functionality. The objective of BLAS++ is to provide a convenient, performance oriented API for development in the C++ language, that, for the most part, preserves established conventions, while, at the same time, takes advantages of modern C++ features, such as: namespaces, templates, exceptions, etc.

DOLFINx is the computational environment of FEniCSx and implements the FEniCS Problem Solving Environment in C++ and Python.

This package provides the C++ interface.

The siemens_to_ismrmrd converter is used to convert data from Siemens raw data format into ISMRMRD raw data format.

Plastimatch is a computer software application which has been designed for volumetric (usually medical) image processing and radiation therapy applications. It can be used for the following purposes:

• Deformable registration

• Atlas-based segmentation

• Image conversion and manipulation

• Vector field conversion and manipulation

• Gamma analysis

• Dose calculation

• Registration analysis (Jacobian)

• Segmentation analysis (Dice, Hausdorff)

A prerequisite for sharing magnetic resonance (imaging) reconstruction algorithms and code is a common raw data format. The ISMRMRD project describes such a common raw data format, which attempts to capture the data fields that are required to describe the magnetic resonance experiment with enough detail to reconstruct images. This package provides a C/C++ library for working with the format.

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.

This package provides a Python library for manipulating data saved as ISMRMRD.

The Gamma Mesh Format (GMF) and the associated library libMeshb provide programers of simulation and meshing software with an easy way to store their meshes and physical solutions. The GMF features more than 200 kinds of data types, like vertex, polyhedron, normal vector or vector solution field. The libMeshb provides a convenient way to move data between those files, via keyword tags, and the user's own structures.

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.

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 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.

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

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.

elastix is an image registration toolbox based on ITK. The software consists of a collection of algorithms that are commonly used to perform (medical) image registration: the task of finding a spatial transformation, mapping one image (the fixed image) to another (the moving image), by optimizing relevant image similarity metrics. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. A command-line interface enables automated processing of large numbers of data sets, by means of scripting.

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

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

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

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.

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.