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)

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.

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.

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

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.

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.

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.

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.

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.

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

NARPS Open Pipelines is a project aimed at reproducing the 70 pipelines from the NARPS study (Botvinik-Nezer et al., 2020) and sharing them as an open resource for the community. It uses Nipype for workflow management and provides templates to facilitate the reproduction of neuroimaging analyses.

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

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

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

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

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.

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

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.

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.

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