Tools

Open-source software I develop for MR spectroscopy. Each is on GitHub and PyPI. Contributions and feedback are welcome.

• 

  Augmentrum

  Data augmentation package for MR spectroscopy.

  A modular framework for creating diverse, physically consistent MRS datasets through flexible augmentation: k-space resampling, coil and average sampling, signal-level perturbations, and synthetic artifacts. Built on the NIfTI-MRS standard with on-the-fly augmentation for PyTorch, TensorFlow, Keras, and JAX.

  CodePyPI
• 

  BasisREMY

  Study-specific basis set generation for MRS.

  A unified framework that generates study-specific basis sets directly from raw MRS data, integrating real pulse shapes and acquisition parameters. It extracts MRSinMRS metadata across vendors, drives multiple simulation backends (FID-A, MRSCloud, FSL-MRS, and more), and exports ready-to-use basis sets with quality-control plots.

  CodePyPI
• 

  PyLCModel

  Python wrapper for LCModel spectral fitting in MRS.

  A lightweight Python wrapper that streamlines least-squares spectral fitting with LCModel. It automates control-file generation, resolves the LCModel binary for you, accepts flexible inputs (NumPy, NIfTI-MRS, jMRUI, .RAW), and parses the full output with single- or multi-core batch fitting.

  CodePyPI