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Fix/pre free surfer pipeline #1

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Fix/pre free surfer pipeline #1

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TakJim
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@TakJim TakJim commented Oct 30, 2024

Pull Request Summary

This PR refactors the processing pipeline for enhanced modularity, flexibility, and improved parameter control in T1w and T2w image processing.

Key Changes

  1. Modular Functions: Created ACPCAlignment, BrainExtraction, T2wToT1wRegAndBiasCorrection, and AtlasRegistration functions, and a main function to control execution flow via RunMode.
  2. Expanded Parameters: Added support for additional phase encodes, patient positioning, and brain extraction settings, improving custom workflow compatibility.
  3. Custom Mask and Existing Data Handling: Improved custom mask application and logic to skip unnecessary steps for existing data.
  4. Enhanced Logging and Structure: Standardized output directory structure and logging, facilitating traceability and maintainability.

TakJim added 12 commits October 31, 2024 04:51
@TakJim
feat: Add support for additional Spin Echo phase encoding directions
1201635
@TakJim
fix: Remove leading whitespace in T1w and T2w input image paths
ecda36d
@TakJim
fix: Set T2wFolder to "NONE" if no T2w images are available and add l…
9047f5b 
…ogging
@TakJim
feat: Add support for custom brain masks and configure default parame…
2120284 
…ters for brain extraction
@TakJim
feat: Add reference volume resampling for T1w and T2w images with dif…
f7a05b2 
…fering resolutions
@TakJim
feat: Enhance gradient nonlinearity correction with orientation adjus…
3ff59f4 
…tments and brain extraction checks
@TakJim
refactor: Modularize ACPC alignment and brain extraction with paramet…
02d2909 
…erized function
@TakJim
refactor: Modularize FNIRT-based brain extraction with new parameters
4743d51
@TakJim
refactor: Modularize T2w to T1w registration with enhanced readout di…
b2ece58 
…stortion correction
@TakJim
feat: Enhance T2w to T1w distortion correction script with additional…
03517ea 
… phase encodes and patient positioning
@TakJim
fix: Correct BiasFieldSmoothingSigma parameter for T1w-only bias fiel…
3834301 
…d correction
@TakJim
refactor: Modularize atlas registration and resampling with main exec…
5fdfd8c 
…ution flow
@TakJim TakJim requested a review from takuya-hayashi October 30, 2024 21:37
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@takuya-hayashi takuya-hayashi takuya-hayashi approved these changes

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@TakJim @takuya-hayashi