Neuroimaging Python Packages

nibabel

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

nipype

Workflows and interfaces for neuroimaging packages

mne

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

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.

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

antspyx

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

pyprep

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

templateflow

A python client to query TemplateFlow via pyBIDS

pydra-freesurfer

Pydra tasks for FreeSurfer designed for Clinica

hedtools

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

pydra-bids

Pydra tasks for BIDS I/O

pydra-petpvc

Pydra tasks for PETPVC designed for Clinica

junifer

Forschungszentrum Jülich Neuroimaging Feature Extractor

nireports

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

nimare

Coordinate- and image-based meta-analysis in Python

netneurotools

Useful tools from the Network Neuroscience Lab

dcm2niix

dcm2nii DICOM to NIfTI converter: compiled versions available from NITRC

tedana

TE-dependent analysis of multi-echo fMRI

neuroglancer-scripts

Conversion of neuroimaging data for display in Neuroglancer

neurocaps

Co-activation Patterns (CAPs) Python package

protocol

generic framework to develop protocols, with an initial focus medical imaging acquisition