Replace the unavailable DeepReg benchmark path with the freesurfer/synthmorph
Docker pipeline for rigid CT-to-T1c registration. Add a shared CT head-box
resample helper for centered initialization and update benchmark docs and CLI
for the new SynthMorph options.
Replace the conda-forge-dependent Elastix CLI path with the pip-installable
ITK-Elastix Python components so the benchmark can run elastix in the main
environment. Add SimpleITK/ITK image and transform conversion helpers, and
use the elastix 5.x EulerTransform rigid pipeline with Mattes MI and ASGD.
Update REGISTRATION_BENCHMARK.md and bench_registration.py documentation to
reflect the new elastix availability, results, and multi-environment merge
workflow. Ignore local elastix output directories in .gitignore.
Update M6 manifest building to register T1c to CT with rigid
Mattes MI on a CT-space head box, including multi-start initial
tilts for large inter-session head motion. The inverse transform
warps CT and GTV into T1c native space, with acceptance based on
concentricity of the warped CT skull ring and MR head silhouette.
Rerun preprocessing when a row has a label but the warped label file
is missing. Normalize volume orientation in read_nii_img.
Add registration benchmark documentation, benchmark script, and
shared registration pipeline helpers.
