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

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.

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

This package provides processing pipelines for structural MRI.

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.

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.

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.

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).

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.

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.

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

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.

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.

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.

This module provides simple, consistent access to package resources.

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 a Pydantic schema for BIDS Stats Models.

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

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.

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.

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.

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

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.

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.