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

templateflow

A python client to query TemplateFlow via pyBIDS

nireports

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

netneurotools

Useful tools from the Network Neuroscience Lab

tedana

TE-dependent analysis of multi-echo fMRI

snirf

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

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.

neuromaps

A toolbox for comparing brain maps

deepslice

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

explorepy

No description available

clinicadl

Framework for the reproducible processing of neuroimaging data with deep learning methods

nidataset

A set of utilities for handling NIfTI datasets, including slice extraction, volume manipulation, and preprocessing of medical imaging data.

frat-brain

Application for ROI fMRI data analysis.

pysnirf2

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

niftiview

View volumetric images in Python 🧠

nipype-ancp

Workflows and interfaces for neuroimaging packages

convert-source

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

quicknat-pytorch

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

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) 🧠

niquery

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