MRS processing Scripts

Basic command-line scripts for Magnetic Resonance Spectroscopy (MRS) data preprocessing using spec2nii and FSL-MRS.

Overview

This repository contains simple bash scripts for:

• Converting vendor-specific MRS formats → NIfTI-MRS
• Splitting dynamic MRS data along the time dimension

Requirements

• Python (≥3.8)
• spec2nii
• FSL-MRS (full installation)

Installation

Install spec2nii: pip install spec2nii

Install FSL-MRS (see official documentation): https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL-MRS

Scripts

1. Conversion (MRS_to_NII)

Converts vendor formats (Philips, Siemens, DICOM, TWIX) to NIfTI-MRS.

2. Dynamic Splitting (MRS_Data_Splitting)

Splits 4D/5D NIfTI-MRS data into individual dynamics using: mrs_tools split

Usage

Edit input/output paths inside each script and run: bash script_name.sh

Notes

• Scripts are intentionally minimal and require manual parameter editing
• Designed for research workflows, not production pipelines

Author

Arijit Bhattacharya
Ph.D. Scholar, Ashoka University OxCIN Global Scholar 2025-2026, The University of Oxford