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Release Notes

0.1.3_7.3.2 [2026-08-20]

Enhancements:

  • Expanded README.md output file documentation with detailed descriptions for gtm.nii.gz, nopvc.nii.gz, mgx.{ctxgm,subctxgm,gm}.nii.gz, Results_4D_T1space_uint16.nii.gz, Results_4D_MNI_uint16.nii.gz, and MNI-space normalized variants.
  • Added freesurfer_license_file as an explicit named input in manifest.json with updated description clarifying it is only required when coreg_method uses FreeSurfer.

Fixes:

  • Added check=True to all sp.run() calls in main.py so failed subprocess commands raise an exception instead of silently continuing.
  • Replaced bare except: with except Exception: in __init__.py to avoid suppressing system-level exceptions.

Maintenance:

  • Migrated from poetry to uv for dependency management, updating pyproject.toml to PEP 621 format with setuptools as the build backend.
  • Upgraded base Docker image from python:3.9 to python:3.11-bullseye and pinned apt package sources to a snapshot.debian.org date for reproducible builds.
  • Added security floor dependencies for some packages to reduce vulnerabilities.
  • Consolidated ANTs build into a single RUN layer and enabled pipefail shell option in Dockerfile to catch download failures.
  • Removed unused imports from some modules.
  • Removed tests/requirements.txt in favor of uv-managed dependencies.
  • Updated manifest.json environment block to reflect PYTHON_VERSION=3.11.13 and added flywheel classification metadata (modality, organ, species, therapeutic area).
  • Standardized gear label to PetSurfer ROI and updated source/url to current GitLab namespace.
  • Updated CONTRIBUTING.md to document uv-based workflow and new pre-commit hooks.

0.1.2_7.3.2 [2023-03-31]

Maintenance:

  • Renamed package from fw-gear-petsurfer-rois to fw-gear-petsurfer-roi for consistency

0.1.1_7.3.2 [2023-03-30]

Enhancements:

  • Added dynamic column naming for PVC uptake CSV output based on selected rescale region instead of hardcoded "pons" reference

Fixes:

  • Fixed CSV column headers to correctly reflect the rescale region used for relative uptake calculations (e.g., PVC_uptake_rel_to_leftcerebralwhitematter instead of always PVC_uptake_rel_to_pons)

Maintenance:

  • Refactored DAT to CSV conversion logic into dedicated convert_dat_to_csv() function
  • Improved code readability by splitting long log messages across multiple lines

0.1.0_7.3.2 [2023-03-28]

Enhancements:

  • Added support for PET ROI analysis with Partial Volume Correction using FreeSurfer's mri_gtmpvc
  • Added support for dynamic (kinetic) analysis with reference region and high-binding region configuration
  • Added configurable point-spread function (PSF) for scanner-specific analysis
  • Added support for Muller-Gartner extended method for voxel-wise analysis
  • Added configurable reference region selection for normalization via FreeSurfer lookup table
  • Added optional MNI template normalization for inter-subject comparison
  • Added 4D visualization files combining T1w and PET analysis results
  • Added orchestrator mode for automated project-level batch processing
  • Added CSV export of ROI statistics from gtm.stats.dat

Maintenance:

  • Added GitLab CI configuration with pre-commit hooks and Docker publishing
  • Added python 3.8+ base image with FreeSurfer 7.3.2 and ANTs 2.4.2
  • Added flywheel-gear-toolkit dependency for Flywheel integration
  • Added pandas for data processing and nibabel for NIfTI file handling
  • Added backoff for robust API retry logic

Documentation:

  • Added comprehensive README with gear overview, inputs, configuration options, and workflow
  • Added CONTRIBUTING.md with development setup instructions
  • Added docs/release_notes.md for tracking version changes
  • Added docs/changelog.md for design decision documentation
  • Added MR template for standardized contribution workflow