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

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.

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.

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.

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.

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.

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.

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.

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

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

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

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

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.

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

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 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.

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

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

DIPY is the paragon 3D/4D+ medical imaging library in Python. It contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.

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

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

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.

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 a Pydantic schema for BIDS Stats Models.