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Fix/pre free surfer pipeline #1

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Fix/pre free surfer pipeline #1

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1201635
feat: Add support for additional Spin Echo phase encoding directions
TakJim Oct 30, 2024
ecda36d
fix: Remove leading whitespace in T1w and T2w input image paths
TakJim Oct 30, 2024
9047f5b
fix: Set T2wFolder to "NONE" if no T2w images are available and add l…
TakJim Oct 30, 2024
2120284
feat: Add support for custom brain masks and configure default parame…
TakJim Oct 30, 2024
f7a05b2
feat: Add reference volume resampling for T1w and T2w images with dif…
TakJim Oct 30, 2024
3ff59f4
feat: Enhance gradient nonlinearity correction with orientation adjus…
TakJim Oct 30, 2024
02d2909
refactor: Modularize ACPC alignment and brain extraction with paramet…
TakJim Oct 30, 2024
4743d51
refactor: Modularize FNIRT-based brain extraction with new parameters
TakJim Oct 30, 2024
b2ece58
refactor: Modularize T2w to T1w registration with enhanced readout di…
TakJim Oct 30, 2024
03517ea
feat: Enhance T2w to T1w distortion correction script with additional…
TakJim Oct 30, 2024
3834301
fix: Correct BiasFieldSmoothingSigma parameter for T1w-only bias fiel…
TakJim Oct 30, 2024
5fdfd8c
refactor: Modularize atlas registration and resampling with main exec…
TakJim Oct 30, 2024
a02af6e
Refactor parameter initialization to use `opts_AddOptional`
TakJim Nov 22, 2024
dd39eae
Refactor main function to streamline RunMode handling
TakJim Nov 22, 2024
3e85592
Update PreFreeSurferPipeline.sh
takuya-hayashi Nov 24, 2024
d9576e9
add CorrectVolumeOrientation
TakJim Nov 26, 2024
e2cd537
Merge branch 'fix/PreFreeSurferPipeline' of https://github.com/RIKEN-…
TakJim Nov 26, 2024
f245f81
feat: Add modularity to PreFreeSurferPipeline with runmode-based cond…
TakJim Dec 10, 2024
fbf4a27
Fix: Correct syntax in imtest command for conditional check
TakJim Dec 10, 2024
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