Code for implementing the Targeted Functional Network Stimulation (TANS) approach described in "Automated optimization of TMS coil placement for personalized functional network engagement", Lynch e…

Tools for analysis of QSM MRI data with QSMbox and SPM

Segmentation tool for the delineation and volumetric quantification of the choroid plexus

U fiber analysis: a toolbox for automated quantification of U-fibers and white matter hyperintensities

Open source framework for pulse sequences

Processing and visualization tools for quantitative MRI data

VISTASOFT is the main software repository of the VISTA lab at Stanford University.

Automated Fiber Quantification

DS6: Deformation-aware learning for small vesselsegmentation with small, imperfectly labeled dataset

This toolbox is dedicated to model fitting and simulation for Intra-Voxel Incoherent Motion (IVIM) MR imaging. It gathers scripts, on the one hand, to fit IVIM bi-exponential signal representation …

python implementation of MRI EPI ghost correction, partial Fourier reconstruction, and other common functions.

Matlab/octave tool to read twix raw data from Siemens MRI scanners.

[IEEE-TMI'23] TaG-Net: Topology-aware Graph Network for Centerline-based Vessel Labeling

Vendor-Agnostic Pulse Sequence Programming with Pulseq: From Basics to Advanced Topics (A Three-Day ISMRM Virtual Meeting Series)

Hongfu Sun's MATLAB codes for QSM reconstruction pipeline.

Matlab GUI pipeline application for quantitative susceptibility mapping (QSM)

Perivascular Space Semi-Automatic Segmentation

Accelerated Microstructure Imaging via Convex Optimization (AMICO) from diffusion MRI data

The open source toolbox for reproducible diffusion MRI-based microstructure estimation

Perivascular (PVS) or Virchow–Robin Spaces (VRS) segmentation with a 3D Unet

Weakly supervised perivascular spaces segmentation with salient guidance of Frangi filter

Single Shell Free Water Elimination Model for Diffusion Tensor Imaging

Reproduce the artice Hoy et al. 2014 Optimization of a free water elimination two-compartment model for diffusion tensor imaging. Neuroimage 103:323-33. doi: 10.1016/j.neuroimage.2014.09.053

Python port of mapVBVD

python file reader/writer for Siemens MRI raw data

methods useful for various MRI recon projects

Michigan Image Reconstruction Toolbox (MIRT) - Matlab version