brkraw-mrs

A BrkRaw converter hook that adds single-voxel MRS support to the BrkRaw ecosystem. This package ports the Bruker MRS workflow from spec2nii and exposes it as a first-party BrkRaw hook.

What it does

• Detects single-voxel MRS scans (PRESS, STEAM, SLASER) from ParaVision metadata
• Reads spectroscopy data from fid or rawdata.job0
• Converts data to NIfTI-MRS (NIfTI-2 preferred) with JSON header extensions

The goal is to make single-voxel MRS data usable within standard MRI analysis workflows supported by BrkRaw.

Install (BrkRaw Hook Standard)

Install the package and register the hook with BrkRaw:

pip install brkraw-mrs
brkraw hook install brkraw-mrs

To install by entrypoint name:

brkraw hook install mrs

To view the hook documentation:

brkraw hook docs brkraw-mrs --render

BrkRaw Usage

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

Support

Tested with Bruker ParaVision standard datasets:

• PV360 3.5-3.7 (PRESS)
• Other MRS sequences and older ParaVision versions are untested

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 provides a foundational implementation of single-voxel MRS support within the BrkRaw framework. Contributions from MRS researchers are encouraged to help validate, refine, and extend the workflow across sequences, acquisition schemes, and ParaVision versions.

Attribution and License

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