Nifti Python Packages

nibabel

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

dcm2niix

dcm2nii DICOM to NIfTI converter: compiled versions available from NITRC

niivue-streamlit

a WebGL2 based medical image viewer. Supports over 30 formats of volumes and meshes.

brainfc

Resting-state fMRI functional connectivity, connectome, brain network and hypergraph analysis in Python with a local GUI. 静息态 fMRI · 功能连接矩阵 · 脑网络 · 超图分析

medh5

Self-describing HDF5 container for one medical imaging sample and all of its ground truth: multi-timepoint, multi-modal images with segmentation, detection, classification and registration annotations, provenance and integrity.

med-imagetools

Transparent and reproducible medical image processing pipelines in Python.

auxiliary

helpful functions for handling biomedical-imaging data in DICOM or NIfTI format

imio

Loading and saving of image data.

zarrnii

Package for working with OME-Zarr and NIFTI images in a unified manner, with a focus on spatial transformations

som

Stanford open modules for python

pydcm

The complete DICOM toolkit for Python — every transfer syntax built in, no plugins, NumPy/PyTorch native, one wheel.

convert-source

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

nii2dcm

nii2dcm: NIfTI to DICOM creation with Python

data-tracking

This project contains scripts to extract metadata from DICOM files, NIFTI files and spreadsheets, and import them into a database.

nekton

A python package for DICOM to NifTi and NifTi to DICOM-SEG and GSPS conversion

pyvoxel

Fast Pythonic data structures and tools for wrangling medical images.

niftiai

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

brain2scalp

Map MNI, Talairach or native-space brain coordinates to their nearest scalp entry point

erwin

Quantitative MRI toolbox in Python

pydcm2niix

dcm2nii DICOM to NIfTI converter: compiled versions available from NITRC

batch-niistats

Calculate descriptive statistics for large numbers of 3D .nii files and return the output as a .csv file. Pure python code that works very quickly on all operating systems.

vids-validator

Open standard for structuring, validating, and delivering annotated medical imaging datasets for AI/ML

nii2png

🖼 A lightweight neuroimaging .nii to .png converter for Matlab and Python users

niftimesh

Watertight, smooth STL reconstruction from NIfTI segmentations (boolean-CSG peel or independent organs).