Brain Imaging Python Packages

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

neuromaps

A toolbox for comparing brain maps

templateflow

A python client to query TemplateFlow via pyBIDS

netneurotools

Useful tools from the Network Neuroscience Lab

snirf

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

nireports

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

tedana

TE-dependent analysis of multi-echo fMRI

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.

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.

deepslice

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

explorepy

Python API for Mentalab biosignal aquisition devices

nidataset

Python package to manage NIfTI images dataset

clinicadl

Open-source Python library for reproducible deep learning in neuroimaging

frat-brain

Application for ROI fMRI data analysis.

convert-source

Converts and organises source MR image data-sets in accordance with the Brain Imaging Data Structure (BIDS)

nipype-ancp

Neuroimaging in Python: Pipelines and Interfaces

n4ax

JAX/GPU N4 bias field correction — a fast drop-in match for ITK N4

niftiview

View volumetric images in Python 🧠

pysnirf2

Interface and validator for SNIRF files

quicknat-pytorch

PyTorch Implementation of QuickNAT and Bayesian QuickNAT, a fast brain MRI segmentation framework with segmentation Quality control using structure-wise uncertainty

niquery

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

hemispec-toolkit

Hemispheric-Specific Brain Modeling and Analysis Based on Generative Adversarial Networks