brkraw-mrs 0.1.2

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

brkraw-mrs

BrkRaw converter hook package for Bruker PRESS SVS (MRS) datasets. 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 PRESS SVS scans (method contains PRESS) 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.

Data ordering for SVS is:

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

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

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

Legacy install script (kept for older workflows):

brkraw-mrs-install

BrkRaw Usage

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

Contributing

This project has not been tested extensively yet. Contributions for validation and improvements are very welcome.

Attribution and License

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