micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below
Ironsmith is a comprehensive, fully automated pipeline for creating and processing Quantitative Susceptibility Maps (QSM), extracting QSM based iron concentrations from subcortical and cortical brain regions and evaluating the quality of QSM data using SNR measures and assessment of outlier regions on phase images.
KUL/UZ NeuroImaging Suite. A set of tools for brain and spine MRI analysis.
Peak width of Skeletonized Mean Diffusivity (PSMD)
Data and tools from the publication "Evolution of Cortical Geometry and its Link to Function, Behaviour and Ecology" by Schwartz et al. for mapping values defined on cortical surfaces between species based on their phylogenetic relationship
Scripts for MRI preprocessing
Shell scripts to run FreeSurfer's recon-all in parallel on multi-core machines. Developed during my time in Christine Ecker's Lab at KGU.
A modified FSL version for use with Slurm
General utility scripts, documentation, and analysis tutorials for Smith Lab.
A sample neuroimaging pipeline for the fMRI data collected by the Aging Brain Cohort.
Why should radiologists rely on eyesight alone, when computer vision and amazing open-source processing frameworks are already available. This respository hosts the full bash-based pipeline, whilst there is a minimal python+webui implementation also available open-source
A simple and intuitive wrapper for FSL tools.
brainlife app - runs AFNI's skullstrip function on NIfTI files
Common Docker Image for the Dosenbach and Greene Labs
Preprocessing pipeline for region of interest selection, linear and non-linear registrations, ICA-based noise rejection, spatial smoothing, and more.
Repository containing files associated with ENIGMA diffusion weighted image preprocessing protocol and instructional video series. Designed by Ryan Cali for the 2022 ReproNim Fellowship Project and the Imaging Genetics Center at the University of Southern California. Questions? Reach out to the author: rcali@loni.usc.edu
Deployment repository for the VUMC Picture tool, responsible for orchestrating the installation and setup of the PICTURE project's core components. This repository automates the deployment process for seamless integration across all related repositories within the PICTURE project.
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