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
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
SynthSeg
Containerized implementation of SynthSeg with additional preprocessing options
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/ITKR
port of ITK to R
cookpa/HD-BETContainer
Docker container for the HD-BET software
cookpa/ANTs
Advanced Normalization Tools (ANTs)
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/bids-examples
A set of BIDS compatible datasets with empty raw data files that can be used for writing lightweight software tests.
cookpa/c3d
Convert3D tool
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/ghBackup
Script to back up your github repositories and wiki using the Github CLI
cookpa/greedyJointLabelFusion
Wrapper script to call greedy for joint fusion
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/ITK-SNAP_Label_Definitions
ITK-SNAP label definition files
cookpa/pybids
Python tools for querying and manipulating BIDS datasets.
cookpa/python-client
A python client to query TemplateFlow via pyBIDS
cookpa/qsiprep
Preprocessing and reconstruction of diffusion MRI
cookpa/qsirecon
Reconstruction of preprocessed q-space images (dMRI)
cookpa/surfplotContainer
Docker container for surfplot
cookpa/surfplotMesa
A package for publication-ready brain surface figures
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/trekker
dMRI based fiber tracking using parallel transport tractography
cookpa/trekkerContainer
Containerized version of trekker