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.

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.

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.

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

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.

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.

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

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

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.

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

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

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.

Nitime contains a core of numerical algorithms for time-series analysis both in the time and spectral domains, a set of container objects to represent time-series, and auxiliary objects that expose a high level interface to the numerical machinery and make common analysis tasks easy to express with compact and semantically clear code.

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.

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).

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.

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.

This package provides a Pydantic schema for BIDS Stats Models.

The nipype1-workflows repository contains legacy workflows from Nipype 1.x, showcasing nearly a decade of development in neuroimaging data processing and analysis.

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

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

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.

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