Philip Cook

Pre-trained models and utilities for deep learning on medical images in PyTorch

Advanced Normalization Tools in Python

Scripts for aligning T1w to ihMT and transferring segmentations to ihMT space or the other way around

Example Jacobian computation from a simple test case using ANTs CreateJacobianDeterminantImage

Docker container for FreeSurfer 5.3

Containerized SynthSeg

Pre-trained models and utilities for deep learning on medical images in Python

Random short scripts to do stuff

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 dimensions.

Advanced Normalization Tools (ANTs)

Tests for handling and applying ANTs transforms

Data and code to test DT warping and reorientation in ANTs

Container building scripts for ANTsX tools

Docker container for the HD-BET software

PipeDream - open source neuroimaging pipelines

Adaptive Riemannian Optimization for Multi-Scale Diffeomorphic Registration

Python tools for querying and manipulating BIDS datasets.

Brain extraction loosely based on antsBrainExtraction.sh, but with different defaults and options

Accelerated Microstructure Imaging via Convex Optimization (AMICO) from diffusion MRI data

Centos 7 container with dev tools for building ANTs

A single NIfTI image saved with all 48 spatial rotation permutations

Containerized SimNIBS, base for Flywheel gear

very basic test of jacobian

Exploring tensor reorientation using ITK transforms

A conda-smithy repository for ants.

MRI brain extraction tool

Just when I thought you couldn’t possibly be any dumber, you go and do something like this… and totally redeem yourself!

Website source

SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages.

Simple bash script that downloads and installs ANTs in a unix environment