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bids-hcp

1.2.8_4.3.0 [2026-05-14]

Maintenance:

  • Initial release of the bids-hcp gear, packaging the HCP Minimal Preprocessing Pipeline for BIDS-structured data including structural (PreFreeSurfer, FreeSurfer, PostFreeSurfer), functional (fMRIVolume, fMRISurface), and diffusion (DiffusionPreprocessing) stages
  • Added multi-stage Dockerfile using uv for Python 3.11 virtual environment management with separate base, build, dev, and prod build targets
  • Added bids-validator@1.9.0 via nodejs 18.x for BIDS validation support
  • Added pyproject.toml with hatchling build backend and dependencies including pybids>=0.14.0,<0.15, flywheel-gear-toolkit>=0.6.6,<0.7, flywheel-bids>=1.2.32,<2, nibabel~=3.0, and numpy==1.23.5
  • Added .gitlab-ci.yml CI configuration using qa-ci gear pipeline template
  • Added .pre-commit-config.yaml with ruff, linting, and pytest hooks
  • Added Singularity/HPC support via tmp_singularity.py for writable directory management in non-Docker environments

Documentation:

  • Added README.md with detailed usage instructions for HCP Structural, Functional, and Diffusion pipeline stages including required inputs, optional inputs, configuration options, and troubleshooting guidance

Maintenance:

  • Introduced layered Dockerfile with separate base, build, dev, and prod stages using uv for Python 3.11 virtual environment management
  • Added bids-validator@1.9.0 via nodejs 18.x in the base image
  • Migrated build system from poetry to hatchling with PEP 621 pyproject.toml
  • Added .dockerignore, .gitignore, .env, .gitlab-ci.yml, and .pre-commit-config.yaml to support CI/CD and development workflows
  • Enabled hadolint and pytest pre-commit hooks
  • Added ruff, ruff_format, ruff_tests, jsonlint, yamllint, and gearcheck pre-commit hooks

Documentation:

  • Added README.md with detailed usage notes for HCP structural, functional, and diffusion preprocessing pipelines

Enhancements

  • Adds HPC support.
  • Fixes some of the issues with the QC scenes.
  • Fixes some env variable issues.
  • Reduced Docker image size.

0.2.4_4.3.0_rc1

Enhancements

  • More robust file handling, particularly around Distortion Correction methods
  • Handles SE-based fmaps with TOPUP (with warning to check validity of the approach)

Documentation

  • More comments to clarify how HCP handles inputs; logic checks

Known issues

  • Structural QC cannot find StrainR/L in the workbench scene provided to the gear
  • Functional QC cannot construct a couple of snapshots, also based on missing files. Note: neither had occurred in previous versions, so perhaps something changed in the base image.

0.2.0_4.3.0

Fixes

  • SSL cert upgraded

Enhancements

  • Logs are produced and saved for all stages run in the analysis
  • Analyses can reliably be continued using previous, structural processing by indicating which hcpstruct.zip to use.
  • Test suite has been added to cover about 75% of the code.
  • Stats_only_struct option allows users to (re)run stats for structural analyses. (Quick summaries, needed for pubs)

Other changes

  • Large-scale refactor of variable names for internal consistency.

Documentation

  • Readme has been revisited and edited.

v0.0.1_4.3.0

Fixes

  • HCP-base image calls the proper workbench URL for download

Enhancements

  • All major processing steps can be accessed from this single gear.
  • The BIDS files are automatically populated from the directory structure.