SMART MRS: A Simulated MEGA-PRESS ARTifacts toolbox for GABA-edited MRS.
Authors
Affiliations (5)
Affiliations (5)
- Department of Biomedical Engineering, University of Calgary, Calgary, Alberta, Canada.
- Department of Radiology, University of Calgary, Calgary, Alberta, Canada.
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada.
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada.
- Department of Electrical and Software Engineering, University of Calgary, Calgary, Alberta, Canada.
Abstract
To create a Python-based toolbox to simulate commonly occurring artifacts for single voxel gamma-aminobutyric acid (GABA)-edited MRS data. The toolbox was designed to maximize user flexibility and contains artifact, applied, input/output (I/O), and support functions. The artifact functions can produce spurious echoes, eddy currents, nuisance peaks, line broadening, baseline contamination, linear frequency drifts, and frequency and phase shift artifacts. Applied functions combine or apply specific parameter values to produce recognizable effects such as lipid peak and motion contamination. I/O and support functions provide additional functionality to accommodate different kinds of input data (MATLAB FID-A.mat files, NIfTI-MRS files), which vary by domain (time vs. frequency), MRS data type (e.g., edited vs. non-edited) and scale. A frequency and phase correction machine learning model experiment trained on corrupted simulated data and validated on in vivo data is shown to highlight the utility of our toolbox. Data simulated from the toolbox are complementary for research applications, as demonstrated by training a frequency and phase correction deep learning model that is applied to in vivo data containing artifacts. Visual assessment also confirms the resemblance of simulated artifacts compared to artifacts found in in vivo data. Our easy to install Python artifact simulated toolbox SMART_MRS is useful to enhance the diversity and quality of existing simulated edited-MRS data and is complementary to existing MRS simulation software.