Philip Cook's repositories
antsInstallExample
Simple bash script that downloads and installs ANTs in a unix environment
antsJacobianExample
Example Jacobian computation from a simple test case using ANTs CreateJacobianDeterminantImage
ANTsXContainers
Container building scripts for ANTsX tools
AMICO
Accelerated Microstructure Imaging via Convex Optimization (AMICO) from diffusion MRI data
HD-BETContainer
Docker container for the HD-BET software
amico-noddi
Containerized wrapper to fit NODDI with AMICO
ANTs
Advanced Normalization Tools (ANTs)
ANTsPy
Advanced Normalization Tools in Python
ANTsPyNet
Medical image analysis framework merging ANTsPy and deep learning
ANTsR
Advanced Normalization Tools in R
ANTsXBratsReg22Singularity
Containerized implementation of
ashs
Automatic Segmentation of Hippocampal Subfields
c3d
Convert3D tool
CuBIDS
Curation of BIDS (CuBIDS): A sanity-preserving software package for processing BIDS datasets.
dStripe
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.media.2021.102255
fdtWrap
Scripts to make calls to topup / eddy and take care of some common pre-requisites
greedyJointLabelFusion
Wrapper script to call greedy for joint fusion
HCPPipelines
A BIDS App for minimal preprocessing using the HCP Pipelines
ITK
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.
ITKMutualInfoSmallVoxelExample
Minimal example demonstrating instability in registration for small voxels (around 1 micron)
PennLINC.github.io
Codebase for github pages website
qsiprep
Preprocessing and reconstruction of diffusion MRI
SynBOLD-DisCo
Synthetic BOLD images for distortion correction of fMRI without additional calibration scans
SynthSeg
Contrast-agnostic segmentation of MRI scans
SynthSegContainer
Containerized SynthSeg
TestITKNIFTI
Test code for reading header information with ITK
trekker
dMRI based fiber tracking using parallel transport tractography