Fix/pre free surfer pipeline#1

Open

TakJim wants to merge 19 commits intoNHP_mergefrom fix/PreFreeSurferPipeline

+528-38

Commits on Oct 30, 2024

feat: Add support for additional Spin Echo phase encoding directions
TakJim
committed
fix: Remove leading whitespace in T1w and T2w input image paths
TakJim
committed
fix: Set T2wFolder to "NONE" if no T2w images are available and add logging
TakJim
committed
feat: Add support for custom brain masks and configure default parameters for brain extraction
TakJim
committed
feat: Add reference volume resampling for T1w and T2w images with differing resolutions
TakJim
committed
feat: Enhance gradient nonlinearity correction with orientation adjustments and brain extraction checks
TakJim
committed
refactor: Modularize ACPC alignment and brain extraction with parameterized function
TakJim
committed
refactor: Modularize FNIRT-based brain extraction with new parameters
TakJim
committed
refactor: Modularize T2w to T1w registration with enhanced readout distortion correction
TakJim
committed
feat: Enhance T2w to T1w distortion correction script with additional phase encodes and patient positioning
TakJim
committed
fix: Correct BiasFieldSmoothingSigma parameter for T1w-only bias field correction
TakJim
committed
refactor: Modularize atlas registration and resampling with main execution flow
TakJim
committed

Commits on Nov 22, 2024

Commits on Nov 24, 2024

Update PreFreeSurferPipeline.sh
takuya-hayashi
authored

Commits on Nov 26, 2024

Commits on Dec 10, 2024