Neuroimaging Python Packages

mne

MNE: Magnetoencephalography (MEG) and Electroencephalography (EEG) in Python

nibabel

Python package to access a cacophony of neuro-imaging file formats

nipype

Workflows and interfaces for neuroimaging packages

nilearn

Machine learning for NeuroImaging in Python

bidsschematools

Brain Imaging Data Structure (BIDS) Specification

mne-bids

MNE-BIDS is a Python package that allows you to read and write BIDS-compatible datasets with the help of MNE-Python.

antspyx

A fast medical imaging analysis library in Python with algorithms for registration, segmentation, and more.

dipy

DIPY is the paragon 3D/4D+ medical imaging library in Python. 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.

braindecode

Deep learning software to decode EEG, ECG or MEG signals

neuromaps

A toolbox for comparing brain maps

pyprep

PyPREP: A Python implementation of the Preprocessing Pipeline (PREP) for EEG data

templateflow

A python client to query TemplateFlow via pyBIDS

dcm2niix

dcm2nii DICOM to NIfTI converter: compiled versions available from NITRC

hedtools

Python validation, summary, and analysis tools for HED (Hierarchical Event Descriptors).

netneurotools

Useful tools from the Network Neuroscience Lab

nimare

Coordinate- and image-based meta-analysis in Python

nireports

The NiPreps' Reporting and Visualization system - report templates and "reportlets"

neuroglancer-scripts

Conversion of neuroimaging data for display in Neuroglancer

junifer

Forschungszentrum Jülich Neuroimaging Feature Extractor

pyradigm

Research data management in biomedical and machine learning applications

pydra-freesurfer

Pydra tasks for FreeSurfer designed for Clinica

dcm2bids

Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure

gradlint

Fast gradient-scheme QC, b-vector flip detection, and repair for diffusion MRI and tractography pipelines.

tedana

TE-dependent analysis of multi-echo fMRI