Release Notes

1.1.2_6.0.2 [2024-04-25]

Enhancements:

Added classification metadata including species (Human), organ (Brain), therapeutic areas (Neurology, Psychiatry/Psychology), modality (MR), and function (Image Processing - Structural)

Fixes:

Maintenance:

Updated base image from flywheel/fsl-base:6.0.1 to flywheel/fsl-base:6.0.2
Migrated from Ubuntu Xenial to Ubuntu Focal
Updated Python command from python to python3 in gear environment setup
Added DEBIAN_FRONTEND=noninteractive argument to suppress installation prompts
Changed gear suite categorization from FSL to Image Processing

Documentation:

Enhanced description with FSL licensing information and academic/commercial use requirements

Enhancements:

Fixes:

Fixed input file basename handling to properly strip .nii.gz and .nii extensions

Maintenance:

Maintenance:

Updated FSL base image from flywheel/fsl-base:5.0.9 to flywheel/fsl-base:6.0.1
Updated FSL installation paths from /usr/share/fsl/5.0 to /usr/share/fsl/6.0
Updated FSL binary paths from /usr/lib/fsl/5.0 to /usr/lib/fsl/6.0

Maintenance:

Maintenance:

Enhancements:

Added validation constraints to betfparam configuration parameter (minimum: 0.01, maximum: 1.0)
Added minimum value constraint (2) to s configuration parameter to prevent singular matrix errors
Enhanced weakbias configuration parameter description to clarify it sets smoothing parameter to 20 internally

Fixes:

Changed betfparam default value from 0 to 0.1 to provide better brain extraction results
Changed s (bias field smoothing) default value from 0 to 10 to avoid singular matrix errors
Updated validation logic to automatically set s to 10 if value is less than 2
Fixed FSL environment path configurations to use correct library locations for 5.0.9

Maintenance:

Downgraded from fsl-base:6.0.1 to fsl-base:5.0.9 Docker base image
Updated FSL directory paths from /usr/share/fsl/6.0 to /usr/share/fsl/5.0
Updated FSL library paths from /usr/share/fsl/6.0/lib to /usr/lib/fsl/5.0
Refactored run.py by extracting utility functions into separate modules (utils/args.py, utils/results.py, utils/log.py)
Replaced inline special character escaping with re.sub() pattern matching
Changed gear execution to use work_dir instead of output_dir for intermediate processing
Introduced context.custom_dict for managing gear-specific state and parameters throughout execution

Enhancements:

Upgraded FSL base image from flywheel/fsl-base:5.0.9 to flywheel/fsl-base:6.0.1
Updated all FSL environment paths from version 5.0 to 6.0 for compatibility with FSL 6.0.1

Fixes:

Fixed typo in run.py where command was incorrectly used instead of command0 in subprocess call for tree output manifest generation

Maintenance:

Updated PATH environment variable to point to /usr/share/fsl/6.0/bin/ instead of /usr/lib/fsl/5.0
Updated LD_LIBRARY_PATH to /usr/share/fsl/6.0/lib for FSL 6.0 library paths
Corrected source repository URL from fsl_anat to fsl-anat
Simplified manifest description to remove verbose pipeline stage details

Enhancements:

Added anatomical image processing pipeline using FSL's fsl_anat tool
Added support for T1-weighted, T2-weighted, and Proton-Density-weighted NIfTI input files
Added configurable pipeline stages including reorientation, cropping, bias-field correction, registration, brain extraction, tissue segmentation, and subcortical structure segmentation
Added automatic zipping of output results with file manifest generation
Added configuration options to selectively disable pipeline stages (nobias, nocrop, nononlinreg, noreg, noreorient, noseg, nosubcortseg)
Added BET brain extraction parameter configuration (betfparam)
Added bias field smoothing parameter (s) and weak bias field mode (weakbias)
Added support for linear registration without search (nosearch)
Added option to preserve intermediate files (nocleanup)
Added automatic handling of filenames with special characters

Maintenance: