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

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.

NiFreeze is a flexible framework for volume-to-volume motion estimation and correction in d/fMRI and PET, and eddy-current-derived distortion estimation in dMRI.

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.

Framework to represent structured directories in python as FileTree objects. File trees can be read in from simple text files describing the directory structure. This is particularly useful for pipelines with large number of input, output, and intermediate files. It can also be used to visualise the data in structured directories using FSLeyes or file-tree on the command line.

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

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

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.

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).

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

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.

The indexed_gzip project is a Python extension which aims to provide a drop-in replacement for the built-in Python gzip.GzipFile class, the IndexedGzipFile. indexed_gzip was written to allow fast random access of compressed NIFTI image files (for which GZIP is the de-facto compression standard), but will work with any GZIP file.

NIPY provides a platform-independent Python environment for the analysis of functional brain imaging data.

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

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

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.

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.

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

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.

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.

Nilearn enables approachable and versatile analyses of brain volumes and surfaces. It provides statistical and machine-learning tools, with instructive documentation & open community.

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.

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.

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.