brkraw-mrs 0.2.0

BrkRaw converter hook for Bruker PRESS SVS NIfTI-MRS outputs (ported from spec2nii)

brkraw-mrs

BrkRaw converter hook package that adds single-voxel MRS conversion support to the brkraw ecosystem. This project ports the Bruker MRS workflow from spec2nii and packages it as a BrkRaw hook so it can be installed and used through BrkRaw's hook tooling.

What It Does

• Detects single-voxel MRS scans (PRESS/STEAM/SLASER by method name) and reads raw spectroscopy data from fid or rawdata.job0.
• Converts interleaved real/imag to complex, infers dimensions, and writes NIfTI-MRS with a header extension JSON (NIfTI-2 preferred).
• Writes a JSON sidecar with NIfTI-MRS metadata for convenience.

The goal is to make single-voxel MRS data usable with the same downstream tools as MRI, so MRS workflows can benefit from the broader BrkRaw ecosystem.

Install (BrkRaw Hook Standard)

Install the Python package, then install the hook assets into BrkRaw:

pip install brkraw-mrs
brkraw hook install brkraw-mrs

To install by entrypoint name:

brkraw hook install mrs

To view the packaged hook docs:

brkraw hook docs brkraw-mrs --render

BrkRaw Usage

brkraw convert \
  /path/to/bruker/PV_dataset \
  --output /path/to/output \
  --sidecar

Support Matrix

Tested datasets are based on the Bruker ParaVision standard datasets: https://www.bruker.com/protected/en/services/communities/pci-community/paravision-versions/paravision-standard-datasets.html

• PV360 3.5 PRESS: conversion tested
• PV360 3.6 PRESS: conversion tested
• PV360 3.7 PRESS: conversion tested
• Older ParaVision versions: not tested
• Other MRS sequences (STEAM, SLASER, others): not tested

Notes: Data ordering for PRESS SVS is assumed as:

(1, 1, 1, n_points, n_averages?, n_dynamics?, n_coils?)

If a dimension is missing or equals 1, it is omitted.

Contributing

This repository is shared as a prototype. The core BrkRaw maintainers are primarily focused on MRI conversion and do not have deep MRS domain expertise. We welcome MRS researchers and developers to validate the workflow and guide ongoing development so it can evolve beyond a single-voxel prototype. Please see CONTRIBUTING.md and start a discussion at: https://github.com/orgs/BrkRaw/discussions/categories/brkraw-mrs

Attribution and License

This hook is a port of the spec2nii Bruker MRS workflow. See NOTICE for attribution details and LICENSE for terms.