Brain Imaging Python Packages

nibabel

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

nilearn

Machine learning for NeuroImaging in Python

nipype

Workflows and interfaces for neuroimaging packages

fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

nireports

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

snirf

Python package for reading, writing and validating Shared Near Infrared Spectroscopy Format (SNIRF) files

tedana

TE-dependent analysis of multi-echo fMRI

fmriprep-docker

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

neuromaps

A toolbox for comparing brain maps

netneurotools

Useful tools from the Network Neuroscience Lab

deepslice

A python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.

cmne

Contextual MEG/EEG source estimation: an LSTM learns the temporal context of brain activity to sharpen dSPM/MNE estimates. PyTorch + ONNX, MNE-Python compatible.

explorepy

Python API for Mentalab biosignal aquisition devices

clinicadl

Open-source Python library for reproducible deep learning in neuroimaging

frat-brain

An analysis tool that uses per-voxel statistical maps in conjunction with FSL atlases to create per-region statistical maps. Current usage includes the creation of regional maps of temporal signal to noise ratio.

nidataset

Python package to manage NIfTI images dataset

pysnirf2

Python package for reading, writing and validating Shared Near Infrared Spectroscopy Format (SNIRF) files

convert-source

Convert source DICOM, PAR REC or NIFTI image data to BIDS directory layout

niftiview

View volumetric images in Python 🧠

mni-to-atlas

A simple Python-based tool for finding brain atlas regions based on MNI coordinates.

niftiai

Train neural nets on 3D images (e.g. MRIs) 🧠

n4ax

JAX/GPU N4 bias field correction — a fast drop-in match for SimpleITK N4 (~2600x faster on A100, <0.2% match)

niftiview-app

Standalone app for viewing volumetric images 🧠 based on Python

niquery

A principled tool to query open neuroimaging datasets, extract relevant information and create new datasets for research