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

Contrast-agnostic segmentation of MRI scans

Spatial Graph Extractor. Library and scripts to study graphs extracted from binary images, or to generate graphs and analyze them completely in-silico. Used at least in biopolymers simulations and …

Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain

MRI brain extraction tool

mrQA: tools for quality assurance in medical imaging datasets, including protocol compliance

Documentation of the scan protocols used to collect the ABCD data

Combined cortical/subcortical atlases for xcp-d and qsiprep

Reproducible and Programmatic Human Neuroimaging Visualisations

Source files for "Learning Statistics with R"

Python functions to convert E-Prime files to csvs. Not currently being developed, but issues and PRs welcome!

Automatic White Matter Bundle Segmentation

A single NIfTI image saved with all 48 spatial rotation permutations

This repository contains code and model weights for the method described in the paper "dStripe: slice artefact correction in diffusion MRI via constrained neural network" https://doi.org/10.1016/j.…

dcm2nii DICOM to NIfTI converter: compiled versions available from NITRC

A Python CLI to execute a collection of deep learning models for brain imaging.

Harmonization tools for multi-site neuroimaging analysis. Implemented as a python package. Harmonization of MRI, sMRI, dMRI, fMRI variables with support for NIFTI images. Complements the work in Ne…

Insight Toolkit (ITK) -- Official Repository. ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dime…

DL+DiReCT - Direct Cortical Thickness Estimation using Deep Learning-based Anatomy Segmentation and Cortex Parcellation

Generate custom Docker and Singularity images, and minimize existing containers

Processing pipelines for the HCP

Brain extraction ANTsRNet app

documentation and experiments to accumulate knowledge about how to segment multivariate imaging data, especially diffusion tensor magnetic resonance imaging of the human brain