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.

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

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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.

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.

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

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

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

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.

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.

Convert3d is a command-line tool for converting 3D images between common file formats. The tool also includes a growing list of commands for image manipulation, such as thresholding and resampling. The tool can also be used to obtain information about image files.

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.

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).

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

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.

This module provides simple, consistent access to package resources.

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

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

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.

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).

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.

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

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.