niworkflows is capable of converting between formats and resampling images to apply transforms generated by the most popular neuroimaging packages and libraries (AFNI, FSL, FreeSurfer, ITK, and SPM).

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.

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.

NiReports contains the two main components of the visual reporting system of NiPreps: 1) reportlets, visualizations for assessing the quality of a particular processing step within the neuroimaging pipeline, and 2) assemblers, end-user write out reportlets to a predetermined folder.

This package provides an implementation of TRX, a tractography file format designed to facilitate dataset exchange, interoperability, and state-of-the-art analyses, acting as a community-driven replacement for the myriad existing file formats.

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.

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

This package provides the Python Client code for accessing neuroimaging templates hosted using TemplateFlow.

NiBabies is an open-source software pipeline designed to process anatomical and functional magnetic resonance imaging data, designed and optimized for human infants between 0-2 years old.

{dcmstack

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

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 utilities for feature analysis, preprocessing and visualization of image quality metrics generated by MRIQC.

The PETPVC toolbox comprises a suite of methods, both classic and more recent approaches, for the purposes of applying PVC to PET data. Eight core PVC techniques are available, and those core methods can be combined to create a total of 22 different PVC techniques.

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

This package provides programs to perform rigid, affine and non-linear registration of 2D and 3D images stored as NIfTI or Analyze formats.

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

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

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.

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.

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.

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.

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.

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