Furen Xiao
16b9828d15
- Added `--clip-ct LO HI` argument to clip CT intensities before registration and scoring, improving A/B comparisons. - Implemented `_clip_image` function to handle intensity clipping of images. - Updated registration functions to utilize CT clipping where beneficial, specifically in `register_niftyreg` and `register_synthmorph`. - Enhanced `fixed_moving` function to ensure CT is always treated as the fixed image. - Introduced Docker support for NiftyReg v2.1.1, including a Dockerfile for building the image. - Updated documentation and help messages to reflect new features and usage instructions. - Adjusted evaluation criteria for registration quality to account for intensity clipping.
35 lines
No EOL
1.5 KiB
Docker
35 lines
No EOL
1.5 KiB
Docker
# NiftyReg v2.1.1 (official KCL-BMEIS Ubuntu release) in Docker.
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#
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# The host (Ubuntu 20.04, glibc 2.31) is too old for the v2.x binaries, which
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# need GLIBC_2.34; the nvidia/cuda ubuntu22.04 base (glibc 2.35) runs them
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# directly. The CUDA runtime provides libcusolver.so.11, which the
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# libniftyreg_cuda.so plugin (dlopen'd by reg_aladin with -platf 1) links
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# against; libcuda.so.1 comes from the host driver via `docker run --gpus all`.
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# Build:
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# docker build -t niftyreg:2.1.1-ubuntu niftyreg/
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# Run (GPU, the pipeline's default):
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# docker run --rm --gpus all -v /path/to/work:/work -w /work \
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# niftyreg:2.1.1-ubuntu -ref ref.nii.gz -flo flo.nii.gz \
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# -rigOnly -aff aff.txt -platf 1
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# Run (CPU fallback):
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# docker run --rm -v /path/to/work:/work -w /work \
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# niftyreg:2.1.1-ubuntu -ref ref.nii.gz -flo flo.nii.gz \
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# -rigOnly -aff aff.txt -platf 0
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# reg_aladin is the ENTRYPOINT, so the NiftyReg CLI flags follow directly.
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# -platf 0|1 = CPU|CUDA, -gpuid selects the device, -omp sets OpenMP threads.
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FROM nvidia/cuda:12.4.1-runtime-ubuntu22.04
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RUN apt-get update && apt-get install -y --no-install-recommends \
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libgomp1 libstdc++6 zlib1g \
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&& rm -rf /var/lib/apt/lists/*
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COPY NiftyReg-Ubuntu-v2.1.1/ /niftyreg/
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# reg_aladin searches /usr/local/lib for the CUDA plugin
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RUN chmod +x /niftyreg/* \
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&& cp /niftyreg/libniftyreg_cuda.so /usr/local/lib/ \
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&& ldconfig
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ENV PATH=/niftyreg:$PATH \
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LD_LIBRARY_PATH=/niftyreg:/usr/local/lib
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ENTRYPOINT ["reg_aladin"] |