Download Example Data

The monai-physio-download-data command downloads example datasets used by MONAI Physio tutorials and demos.

Supported Datasets

Data name	Description
`Slicer-Heart-CT`	Public 4D cardiac CT sample from SlicerHeart.
`KCL-Heart-Model`	King’s College London four-chamber heart model dataset: 20 individual heart meshes plus an average mesh, from Zenodo.
`CHOP-Valve4D`	CHOP Jolley Lab transcatheter pulmonary valve model, converted from the original FEBio model to VTK/ITK and segmented with Simpleware, from the MONAI Physio GitHub release. See `data/CHOP-Valve4D/README.md`.
`Chest-CT`	Ungated 3D chest CT, a single static volume, from the MONAI Physio GitHub release. See `data/Chest-CT/README.md` for the data source and required citation.
`TCIA-4DLung`	Converted tutorial subset of the 4D-Lung collection, from the MONAI Physio GitHub release. See `data/TCIA-4DLung/README.md` for the data source, the full-collection manual download, and required citation.
`Duke-Heart-4DLabelmaps`	Gated 4D cardiac labelmaps and JSON landmark files from the PROMISE study CT data (Duke University, Dr. Paul Segars’ lab), segmented with the ASCardio module of Simpleware, from the MONAI Physio GitHub release. Models trained on them should only be applied to labelmaps also generated with ASCardio (`SegmentHeartSimplewareTrimmedBranches`). See `data/Duke-Heart-4DLabelmaps/README.md`.
`PhysicsNeMo-MGN-Lung-Motion`	Pretrained PhysicsNeMo MeshGraphNet checkpoint for lung motion, from the MONAI Physio GitHub release. Used by Lung Tutorial 10 and later when skipping Tutorial 9’s training.

Basic Usage

Download a dataset into its default location:

monai-physio-download-data Slicer-Heart-CT

Running the command with no arguments prints usage/help instead of downloading anything.

Options

monai-physio-download-data [Slicer-Heart-CT|KCL-Heart-Model|CHOP-Valve4D|Chest-CT|TCIA-4DLung|Duke-Heart-4DLabelmaps|PhysicsNeMo-MGN-Lung-Motion] [--directory DIRECTORY]

data_name: Dataset to download. One of Slicer-Heart-CT, KCL-Heart-Model, CHOP-Valve4D, Chest-CT, TCIA-4DLung, Duke-Heart-4DLabelmaps, or PhysicsNeMo-MGN-Lung-Motion. Required - omitting it prints help and exits.
--directory: Directory where the dataset is stored. Defaults to data/<data_name>.

Output

For Slicer-Heart-CT, the command downloads the 4-D sequence and splits it into per-phase 3-D volumes:

data/Slicer-Heart-CT/TruncalValve_4DCT.seq.nrrd
data/Slicer-Heart-CT/slice_000.mha ... slice_020.mha

The command uses monai_physio.download_data.DownloadData.DownloadSlicerHeartCTData(), so repeated runs reuse the existing non-empty file and skip the split once the slice_???.mha files are present.

For KCL-Heart-Model, the command downloads, extracts, and reuses:

data/KCL-Heart-Model/average_mesh.vtk
data/KCL-Heart-Model/input_meshes/01.vtk ... 20.vtk

The command uses monai_physio.download_data.DownloadData.DownloadKCLHeartModelData(), which fetches each per-model .tar.gz archive from Zenodo, extracts its mesh, and skips archives whose target .vtk file is already present.

For CHOP-Valve4D, the command downloads, extracts, and reuses:

data/CHOP-Valve4D/Alterra/   (valve mesh time series, >1 GB)
data/CHOP-Valve4D/TPV25/     (valve mesh time series, >1 GB)
data/CHOP-Valve4D/CT/        (source CT volume and Simpleware segmentation)

The command uses monai_physio.download_data.DownloadData.DownloadCHOPValve4DData(), which fetches each subdirectory’s zip archive from the MONAI Physio GitHub release and skips a subdirectory once it has its expected extracted files (the CT volume or Simpleware segmentation for CT/, .vtk meshes for Alterra/ and TPV25/) - a subdirectory left behind by an interrupted extraction is re-downloaded rather than treated as complete.

For Chest-CT, the command downloads and reuses a single volume:

data/Chest-CT/Chest-CT.mha

The command uses monai_physio.download_data.DownloadData.DownloadChestCTData(), which fetches the volume from the MONAI Physio GitHub release and reuses an existing non-empty file, so re-running resumes an interrupted download.

For TCIA-4DLung, the command downloads, extracts, and reuses:

data/TCIA-4DLung/100_HM10395/100_HM10395_g000.nii.gz ...
data/TCIA-4DLung/116_HM10395/116_HM10395_g000.nii.gz ...

The command uses monai_physio.download_data.DownloadData.DownloadTCIA4DLungData(), which fetches both zip archives (TCIA-4DLung-Part1.zip and TCIA-4DLung-Part2.zip) from the MONAI Physio GitHub release and skips the download entirely once any case’s phase volumes are already present - this is a converted tutorial subset; see data/TCIA-4DLung/README.md for how to obtain the full TCIA 4D-Lung collection manually.

For Duke-Heart-4DLabelmaps, the command downloads, extracts, and reuses:

data/Duke-Heart-4DLabelmaps/pm0002/*_labelmap.nii.gz
data/Duke-Heart-4DLabelmaps/pm0002/*_landmark.mrk.json ...

The command uses monai_physio.download_data.DownloadData.DownloadDukeHeart4DLabelmapsData(), which fetches Duke-Heart-4DLabelmaps.zip from the MONAI Physio GitHub release and skips the download once any case’s labelmaps are already present.

For PhysicsNeMo-MGN-Lung-Motion, the command downloads, extracts, and reuses:

tutorials/network_weights/physicsnemo_mgn_lung_motion/mgn_stage_model.pt
tutorials/network_weights/physicsnemo_mgn_lung_motion/  (other epoch
    checkpoints and metadata)

The command uses monai_physio.download_data.DownloadData.DownloadPhysicsNeMoMGNLungMotionData(), which fetches physicsnemo_mgn_lung_motion.zip from the MONAI Physio GitHub release and skips the download once mgn_stage_model.pt is already present. Unlike every other dataset, its default --directory is tutorials/network_weights, not data/<data_name>.

Download Example Data

Supported Datasets

Basic Usage

Options

Output

See Also