Non-Water-Suppressed Spectroscopy

Code and Example Data for GIRF-Corrected Non-Water-Suppressed Single-Voxel-Spectroscopy

Citation: J. B.Bacon, P.Jezzard, and W. T.Clarke, “MR Spectroscopy Without Water Suppression Using the Gradient Impulse Response Function,” Magnetic Resonance in Medicine (2026): 1–12, https://doi.org/10.1002/mrm.70383.

Installation and Dependencies

Clone this repositry using

git clone https://github.com/jbbacon/NWS_Spectroscopy.git

Create a conda environment to install the relevant dependencies and activate it

conda create --name nws_spec
conda activate nws_spec

Install fsl_mrs version 2.4.9, and appropriate ipython dependcies into the envrionment

conda install -c conda-forge -c defaults -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ fsl_mrs=2.4.9
conda install -c conda-forge nbformat ipykernel ipympl ipywidgets

Contents and Usage

Each notebook is self containing and can be run without requiring any local edits. The output of each notebook is the input to the following notebook as described below. Example data is provided for each stage except for preprocessing.

Preprocessing

Data is not made available for this step.

1. Process raw TWIX data using spec2nii.

2. Preprocessing is performed using either sLaser_preproc.ipynb or mPress_preproc.ipynb, depending on the spectroscopy acquisiton. These notebooks implement standard preprocessing steps; RF coil combination, retrospective correction of frequency and phase drifts, signal averaging, automated frequency and phase correction.

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GIRF Correction

This step performs the GIRF correction and results in the removal of the eddy current sidebands.

GIRF correction of the non-water-suppressed spectroscopy data is performed using

• sLASER_GIRF_correction.ipynb
• mPRESS_GIRF_correction.ipynb

Preprocessed data for one representative participant is provided in

• ./Data_for_correction/sLaser_preproc
• ./Data_for_correction/sLaser_preproc

Corresponding input gradient waveforms required for the GIRF Correction are provided in

• ./Data_for_correction/gradients_sLaser
• ./Data_for_correction/gradients_mPRESS

GIRF measurments are available in

• ./GIRF_measurements

Full code for the measurement and calculation of the GIRF is available at https://github.com/jbbacon/GIRF_PE_Python. The GIRF measurment provided here is the outcome of following all the steps in that repositrory.

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Water Modelling and Data Fitting

This steps performs metabolite fitting for the water-suppressed reference spectra and the GIRF-corrected non-water-suppressed spectra.

Modelling of the water peak and fitting of the underlying metabolites is performed in

• sLaser_fitting.ipynb
• mPress_fitting.ipynb

GIRF-corrected data is available for all participants in

• ./Data_for_fitting

Optionally, final results are output to ./Data_for_plotting for use in making figures. This step has been completed in full for one participant.