High-Resolution 4D CT Reconstruction

The physiomotion4d-reconstruct-highres-4d-ct command reconstructs a high-resolution 4D CT time series from ordered phase images and a high-resolution reference image.

Input Requirements

Ordered 3D phase images, such as .mha, .mhd, .nrrd, or .nii.gz files.
A fixed high-resolution reference image.
Optional fixed and moving masks for registration focus.

DirLab-4DCT data cannot be downloaded automatically by PhysioMotion4D. Prepare it manually before using the DirLab tutorial or examples.

Basic Usage

physiomotion4d-reconstruct-highres-4d-ct \
    --time-series-images frame_*.mha \
    --fixed-image highres_reference.mha \
    --output-dir ./results

With Upsampling

physiomotion4d-reconstruct-highres-4d-ct \
    --time-series-images frame_000.mha frame_001.mha frame_002.mha \
    --fixed-image highres_reference.mha \
    --reference-frame 0 \
    --upsample \
    --output-dir ./results

Registration Options

physiomotion4d-reconstruct-highres-4d-ct \
    --time-series-images frame_*.mha \
    --fixed-image highres_reference.mha \
    --registration-method ants \
    --ants-iterations 30 15 7 3 \
    --prior-weight 0.5 \
    --output-dir ./results

Outputs

The command writes reconstructed images to --output-dir using --output-prefix as the filename prefix. Use --save-transforms and --save-losses when registration diagnostics are needed.

Python API

Use physiomotion4d.WorkflowReconstructHighres4DCT for programmatic access.