A curated list of open-source tools, libraries, datasets, tutorials, and communities for MRI physics, pulse sequence development, image reconstruction, MR spectroscopy, quantitative MRI, and neuroimaging workflows.
This list is intended for researchers, students, MRI physicists, engineers, and imaging scientists working across preclinical and clinical MRI.
- Pulse Sequence Development
- Reconstruction
- MR Spectroscopy
- Quantitative MRI
- Diffusion MRI
- fMRI and Neuroimaging
- Data Conversion and Standards
- Visualization and Analysis
- Phantoms, Simulation, and Education
- Datasets
- Communities and Learning
- Contributing
- Pulseq — Open framework for MR pulse sequence design and execution.
- Pulseq Tutorials — Practical examples for learning Pulseq.
- PyPulseq — Python tools for creating Pulseq-compatible sequences.
- GPI Pulseq examples — Visual programming ecosystem used in some MR research workflows.
- BART — Berkeley Advanced Reconstruction Toolbox for computational MRI.
- Gadgetron — Streaming reconstruction framework for MRI.
- ISMRMRD — Raw MR data format and tools for reconstruction workflows.
- SigPy — Iterative methods and signal processing for imaging reconstruction.
- Michigan Image Reconstruction Toolbox (MIRT) — Reconstruction algorithms and educational material.
- FSL-MRS — End-to-end magnetic resonance spectroscopy analysis.
- Gannet — MATLAB toolkit for edited 1H MRS analysis.
- Osprey — Open-source toolkit for MRS data processing and quantification.
- spant — R package for MRS analysis.
- FID-A — Simulation and processing tools for MRS and RF pulse design.
- qMRLab — Quantitative MRI analysis framework.
- hMRI Toolbox — Quantitative MRI workflows in SPM.
- MRtrix3 — Widely used toolkit for diffusion MRI and related quantitative analyses.
- DIPY — Diffusion MRI analysis in Python.
- MRtrix3 — Diffusion modelling, tractography, and processing.
- QSIPrep — Reproducible diffusion MRI preprocessing pipelines.
- fMRIPrep — Standardized fMRI preprocessing.
- NiBabel — Access to common neuroimaging file formats in Python.
- Nilearn — Statistical learning and visualization for neuroimaging.
- FreeSurfer — Structural neuroimaging analysis.
- AFNI — Analysis and visualization for functional MRI.
- FSL — Neuroimaging analysis library and tools.
- dcm2niix — DICOM to NIfTI conversion.
- BIDS — Brain Imaging Data Structure standard.
- heudiconv — DICOM conversion and BIDS organization.
- BIDS Validator — Validation for BIDS datasets.
- 3D Slicer — Medical image visualization and analysis platform.
- ITK — Toolkit for medical image analysis.
- SimpleITK — Simplified interface to ITK.
- napari — N-dimensional image viewer.
- JEMRIS — MRI simulation platform.
- Bloch Solver — GPU-accelerated Bloch simulation.
- MRzero — MRI simulation and education framework.
- Awesome Neuroimaging — Broad neuroimaging resource collection.
- fastMRI — Accelerated MRI dataset and benchmarks.
- OpenNeuro — Shared neuroimaging datasets.
- IXI Dataset — Public structural MRI dataset.
- Human Connectome Project — Large-scale human neuroimaging resource.
- ISMRM — International Society for Magnetic Resonance in Medicine.
- OHBM — Organization for Human Brain Mapping.
- NeuroStars — Community Q&A for neuroimaging.
- Pulseq Tutorials — Good starting point for sequence development.
Contributions are welcome. Please open a pull request to:
- add a tool or library,
- improve a description,
- fix a broken link,
- suggest a new category, or
- add educational resources and example datasets.
Please ensure that additions are:
- Relevant to MRI physics, MRI engineering, MRS, reconstruction, pulse sequence programming, or closely related imaging workflows.
- Open-source or openly accessible.
- Actively useful to researchers, students, or developers.
- Added with a short, neutral description.
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