Release Notes

0.2.1_7.4.1 [2024-09-27]

Fixes:

Fixed Dockerfile entrypoint to use absolute path /flywheel/v0/run.py instead of environment variable expansion

Enhancements:

Added support for control points file input to enable manual intensity correction and re-running recon-all with updated parameters
Added rois_in_output configuration option to optionally output ROIs directly instead of only in zip archives
Added mniroizip input validation to check file format, dimensions, and NIfTI compatibility before processing
Added zipinfo.csv generation for all output zip files to provide detailed archive metadata
Enhanced MNI ROI handling to support both gear-provided and user-provided ROIs with flexible combinations via mni_rois config option

Fixes:

Fixed thalamic nuclei segmentation to use consistent version (v13) instead of wildcard pattern
Fixed hippocampal segmentation to properly handle both T1 and T2 inputs
Fixed aparc2009 ROI separation to handle both brainmask.mgz and brain.mgz files for compatibility with different Freesurfer versions
Fixed MACOSX metadata file removal from user-provided zip files
Fixed MNI ROI template path handling and dimension validation

Maintenance:

Migrated from freesurfer 7.3.2 to 7.4.1
Migrated from ants v2.4.2 and freesurfer 7.3.2 embedded builds to multi-stage Docker build using flywheel/rtp2_ants:0.1.0_2.4.2 and flywheel/freesurfer:0.1.0_7.4.1 pre-built images
Migrated from flywheel-gear-toolkit to support work directory separation from output directory
Updated pandas to ^2.2.2 and urllib3 to 1.26.18 for security patches
Reorganized Dockerfile to use multi-stage builds and optimize layer caching
Consolidated environment variables and reduced image size through layer optimization
Updated .gitlab-ci.yml to reference flywheel-io/tools/etc/qa-ci instead of sse-qa-ci
Reorganized template files and moved ROI-related files to templates/ directory
Removed merge request template in .gitlab/merge_request_templates/

Documentation:

Updated README with detailed descriptions of all inputs, configuration options, and outputs
Added clarification for control_points input requirements and usage
Enhanced mniroizip input documentation with validation requirements and download links
Updated configuration descriptions to explain re-run behavior and control point integration

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Enhancements:

Added FreeSurfer recon-all execution with multi-T1w and T2w support
Added automated segmentation of hippocampal subfields
Added brainstem structures segmentation
Added thalamic nuclei parcellation with FRAC correction algorithm
Added cerebellum parcellation using Buckner 2011 atlas
Added Glasser HCP atlas integration for cortical parcellation
Added MORI JHU white matter tract ROIs
Added Neuropythy analysis for visual cortex mapping (Benson14, Wang15 atlases)
Added aparc.a2009s segmentation with individual ROI extraction
Added ANTs registration pipeline for MNI space transformations
Added support for custom surface annotations (annot files) with conversion to volumetric ROIs
Added gtmseg execution for PETsurfer compatibility
Added automatic conversion of segmentation outputs to NIfTI format
Added CSV export for all segmentation statistics
Added support for pre-run FreeSurfer input via zip file

Maintenance:

Initial project setup with Docker environment configuration
Added build system with poetry for dependency management
Configured CI/CD pipeline with GitLab CI for testing and Docker publishing
Added pre-commit hooks for code quality (black, isort, pytest, markdownlint, yamllint)
Installed python 3.9.15 runtime environment
Installed FreeSurfer 7.3.2 and ANTs v2.4.2 for neuroimaging analysis
Added MATLAB Runtime (MCRv97) for brainstem and hippocampal subfield modules
Configured required dependencies: flywheel-gear-toolkit>=0.6, flywheel-sdk>=16.8.0, numpy>=1.23.4, scipy>=1.9.3, nilearn>=0.9.2, nibabel>=4.0.2, neuropythy>=0.12.5, pybids>=0.15.4

Documentation: