Gannet v3.5.0 released

MRS Software Gannet
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Download Gannet v3.5.0

New features

  • Gannet is now compatible with BIDS
    • bids-matlab, a MATLAB toolkit for interfacing with BIDS datasets, is embedded in Gannet, and users can now input BIDS datasets directly into GannetLoad.m (see documentation for usage instructions)
  • Added image QA metrics based on MRIQC
    • GannetSegment.m now calculates and saves the following QA metrics for each anatomical image:
      • Signal-to-noise ratio (SNR) of GM, WM, CSF, and the whole brain (two variants: one using the median absolute deviation of the air background based on Dietrich et al. (2007), and one using the standard deviation of the noise within the tissue class)
      • Contrast-to-noise ratio (CNR) between GM and WM
      • Coefficient of variation (CV) of GM and WM
      • Coefficient of joint variation (CJV) between GM and WM
      • Entropy-focus criterion (EFC)
      • Foreground-background energy ratio (FBER)
      • WM to maximum intensity ratio (WM2MAX): the median intensity within WM over the 95% percentile of the full intensity distribution, that captures the existence of long tails due to hyper-intensity of the carotid vessels and fat
    • These metrics are saved in MRS_struct.out.QA
  • Added GitHub Actions for continuous integration with bids-matlab, dicm2nii, and export_fig to ensure compatibility with the latest versions of these dependencies
  • Added dependabot.yml to automatically check for updates to GitHub Actions
  • Water-unfiltered (but aligned) spectra are now saved in MRS_struct
  • All version strings (e.g., MRS_struct.version.*) are now stored under MRS_struct.info.version.*, and datetime stamps for processing steps are added as MRS_struct.info.datetime.*

Major changes

  • When calculating GM, WM, and CSF fractions in GannetSegment.m, the probabilistic tissue maps are now thresholded at 0.9 before calculating the fractions. This should improve the accuracy of tissue fraction estimates

Minor changes

  • Modified SiemensTWIXRead.m to use iceParam for pointsBeforeEcho in MEGA-sLASER, aligning with MEGA-PRESS handling for consistency
  • Changed the naming convention for water residual fit results from ResidWater to resid_water in GannetFit.m for consistency
  • Improved input argument validation and error messages, including checks for cell array inputs and file existence, with clearer error output for missing files
  • Updated export_fig to v3.52
  • Updated dicm2nii to v2025.08.21
  • MANY COSMETIC CHANGES to improve code readability and maintainability

Full Changelog: v3.4.0...v3.5.0

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