Atlas-based Imaging Data Analysis Pipeline (AIDA) for structural and functional MRI of the mouse brain

This repository contains Standard MRI phantom datasets from Bruker ParaVision 360 v3.6. It includes 14 image sequences (k-space, reconstructed, headers, DICOM, and NIFTI files) to help developers t…

Implementation of the BSS-rPCA by Song et al (2020) for MWI using mGRE MRI data.

Label Augmented Modality Agnostic Registration (LAMAReg) is a MRI resgistration technique combines deep learning-based segmentation and numerical solutions to generate precise non linear warpfields

Github Repo for "DeepFDR: A Deep Learning-based False Discovery Rate Control Method for Neuroimaging Data"

Adaptive Riemannian Optimization for Multi-Scale Diffeomorphic Registration

Odense-Oxford PET Image Analysis toolbox (Published in the NeuroImage journal)

Myelin mapping test-retest study

Generate design matrices, contrasts, and scripts to set up FSL randomise analyses.

Data and code supporting Hansen et al., 2025, bioRxiv "Synaptome architecture shapes regional dynamics in the mouse brain"

A growing collection of bioinformatics tutorials, project guides, tools, and articles I’ve developed to make bioinformatics more accessible.

Neuroimaging based brain age prediction using 3D Dense-net

Code to perform Scaled Subprofile Model (SSM), a principal components analysis (PCA)-based spatial covariance method.

utilities for processing modalities beyond T1w

Sex matters: the MouseX DW-ALLEN Atlas and Parcellation for mice diffusion-weighted MR imaging

BrainAGE Estimation

A list of brain imaging datasets with multiple scans per subject. Feel free to update the list via 'pull requests'!

Bayesian analysis + tidy data + geoms (R package)

Contrast Coding Utilities

DAGs with NO TEARS: Continuous Optimization for Structure Learning

A Python 3 package for learning Bayesian Networks (DAGs) from data. Official implementation of the paper "DAGMA: Learning DAGs via M-matrices and a Log-Determinant Acyclicity Characterization"

Flexible DICOM conversion into structured directory layouts

Framework for the reproducible classification of Alzheimer's disease using machine learning

Processing pipelines for the HCP

QSMxT is an end-to-end software toolbox for Quantitative Susceptibility Mapping.