Pinned Repositories
ANTs
Advanced Normalization Tools (ANTs)
antsDTOrientationTests
Data and code to test DT warping and reorientation in ANTs
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
antsPseudoGeodesicJointFusion
Shortcut to do joint fusion by using an intermediate template to warp atlases to the target image
ANTsXContainers
Container building scripts for ANTsX tools
fwKeySecurity
Details of how to prevent and detect leaks of Flywheel API keys in code
HD-BETContainer
Docker container for the HD-BET software
pipedream
PipeDream - open source neuroimaging pipelines
antsct-aging
ANTs cortical thickness pipeline container, contains a template for older individuals
cookpa's Repositories
cookpa/antsInstallExample
Simple bash script that downloads and installs ANTs in a unix environment
cookpa/antsJacobianExample
Example Jacobian computation from a simple test case using ANTs CreateJacobianDeterminantImage
cookpa/ANTsXContainers
Container building scripts for ANTsX tools
cookpa/AMICO
Accelerated Microstructure Imaging via Convex Optimization (AMICO) from diffusion MRI data
cookpa/HD-BETContainer
Docker container for the HD-BET software
cookpa/amico-noddi
Containerized wrapper to fit NODDI with AMICO
cookpa/ANTs
Advanced Normalization Tools (ANTs)
cookpa/antsct-aging-fw
cookpa/ANTsPy
Advanced Normalization Tools in Python
cookpa/ANTsPyNet
Pre-trained models and utilities for deep learning on medical images in Python
cookpa/antsPyRegistrationStability
Experiments to examine the reproducibility/stability of ants and antspy registration
cookpa/ANTsXBratsReg22Singularity
Containerized implementation of
cookpa/ashs
Automatic Segmentation of Hippocampal Subfields
cookpa/ashsthk
cookpa/c3d
Convert3D tool
cookpa/CuBIDS
Curation of BIDS (CuBIDS): A sanity-preserving software package for processing BIDS datasets.
cookpa/dicom-mr-classifier
cookpa/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
cookpa/fdtWrap
Scripts to make calls to topup / eddy and take care of some common pre-requisites
cookpa/greedyJointLabelFusion
Wrapper script to call greedy for joint fusion
cookpa/HCPPipelines
A BIDS App for minimal preprocessing using the HCP Pipelines
cookpa/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.
cookpa/ITKMutualInfoSmallVoxelExample
Minimal example demonstrating instability in registration for small voxels (around 1 micron)
cookpa/PennLINC.github.io
Codebase for github pages website
cookpa/qsiprep
Preprocessing and reconstruction of diffusion MRI
cookpa/SynBOLD-DisCo
Synthetic BOLD images for distortion correction of fMRI without additional calibration scans
cookpa/SynthSeg
Contrast-agnostic segmentation of MRI scans
cookpa/SynthSegContainer
Containerized SynthSeg
cookpa/TestITKNIFTI
Test code for reading header information with ITK
cookpa/trekker
dMRI based fiber tracking using parallel transport tractography