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fwkeysecurity

Details of how to prevent and detect leaks of Flywheel API keys in code

gitsecretsfwdemo

Example of using git-secrets to keep Flywheel API keys safe

greedy

Very fast greedy diffeomorphic registration code

greedyjointlabelfusion

Wrapper script to call greedy for joint fusion

greedyoptimizeparams

Experiments to improve greedy JLF performance

hcppipelines

A BIDS App for minimal preprocessing using the HCP Pipelines

hd-betcontainer

Docker container for the HD-BET software

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)

labelstats

Wrapper for applying c3d label statistics on batches of images

pennlinc.github.io

Codebase for github pages website

picslbib

PICSL lab bibliography

pipedream

PipeDream - open source neuroimaging pipelines

qsiprep

Preprocessing and reconstruction of diffusion MRI

smt

Microscopic diffusion anisotropy imaging made easy!

socialdefeat

R package for analysis of social defeat data

stackslices

Scripts using ANTs and c3d to extract slices from series of 4D or 3D volumes, adjust contrast, and make animations

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

utilities