Change log and model updates

Segmentation models in MuscleMap are periodically retrained on expanded and more diverse datasets to optimise performance, robustness, and cross-site generalisability.

All notable changes to MuscleMap are listed below.
Source: GitHub Releases

v2.0 Latest

  • Refactors MuscleMap to load model parameters and template NIfTI files directly from Zenodo instead of bundling them in the repository
  • Added Zenodo download logic in mm_util.py with support for multiple Zenodo versions
  • Updated mm_gui.py and mm_segment.py to use the new Zenodo-based model loading
  • Added mm_qc_gui.py as a new QC interface
  • Updated setup.py and requirements.txt for v2.0 dependencies
  • Updated .gitignore to exclude large model files
  • Updated README.md with instructions for Zenodo usage and template file setup

v1.3

  • Included auto chunking to estimate a safe chunk size from currently available CPU or GPU memory and keeps extra headroom to reduce OOM failures
  • Included new model parameters
  • Included extra spatial padding to preserve higher accuracy at muscle boundaries in cropped images
  • Note: Model weights (.pth) and configuration files (.json) for mm_segment have been removed from the git history to reduce repository size. To use this release, download the model parameters from Zenodo and place them in the corresponding subfolder, e.g. scripts/models/wholebody/ or scripts/models/abdomen/
  • Note: Template images (.nii.gz) for mm_register_to_template have been removed from the git history to reduce repository size. To use this release, download the template images from Zenodo and place them in the corresponding subfolder, e.g. scripts/templates/abdomen/

v1.2

  • Included 10 more muscles in wholebody model (left and right pectineus, obturator externus, obturator internus, piriformis, gemelli and quadratus femoris)
  • Included more training data for wholebody model

v1.1

  • Trained whole-body model on a more diverse dataset to improve generalizability
  • Now using foreground cropping to improve inference efficiency

v1.0

  • Added the whole-body segmentation model (v1.0)
  • Improved handling of large images in mm_segment
  • Added new options to mm_segment
  • Cleaned and improved mm_extract_metrics

v0.3 Pre-release

  • Introduced version numbers for trained models
  • Preparation for the v1.0 release

v0.2 Pre-release

  • Added mm_register_to_template for anatomical registration

v0.1 Pre-release

  • Initial public pre-release including:
    • mm_segment
    • mm_extract_metrics
    • mm_gui

v0.0 Pre-release

  • Initial repository version with early segmentation tools

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