New toolboxes, segmentation workflow and Muscle-BIDS pipeline

What's new in QMRITools 5

A summary of the changes since version 4

QMRITools 5 requires Wolfram Language 15.0 or newer. The complete list of changes, per major version, is in the changelog.

New toolboxes

  • NeuralNetworkTools: building blocks for neural networks, loss layers, transfer learning and inspection of trained networks.
  • ShapeTools: statistical shape models and meshes of segmented structures.
  • AmaresTools: AMARES fitting of MR spectroscopy data.

Muscle segmentation

  • Complete train-and-deploy workflow with new architectures (UNET++, strided convolutions), training on multiple contrasts, masked pretraining and encoder freezing for transfer learning, and parallel data loading.
  • More anatomy, including the shoulder, and merging of segmentations.
  • Segmentation confidence maps and QC plots.
  • Command line scripts for installing QMRITools and segmenting data without Mathematica.

See automated muscle segmentation.

Muscle-BIDS

  • An end-to-end pipeline from DICOM to per-muscle results, including T2 mapping, tractography and MuscleBidsAnalysis.
  • Better DICOM conversion with multiple sessions and repeated scans, combining of config files and batch processing.
  • Integration with MuscleMap.
  • A new manual with example configurations.

See Muscle-BIDS.

Diffusion, tractography and fasciculation

  • Random permeable barrier model (RPBM) fitting, correction for gradient non-linearity and export of b-values and b-vectors.
  • Import and export of MRtrix .tck files and tract length and curvature measures.
  • Area based activation sizes for fasciculation analysis.

Denoising, reconstruction, spectroscopy and simulation

  • Self-supervised network denoising (P2SDenoise), harmonic denoising of tensors and denoising of spectroscopic imaging data.
  • More reconstruction options: prewhitening, SENSE smoothing and weighting, k-space averaging.
  • SpectraSimulator and EPG simulation that accounts for the refocusing pulse phase.

Plotting