Converting to USD#

The conversion process involves three stages:

NRRD to NIfTI Conversion

  • Convert segmentation files from NRRD to NIfTI format

NIfTI to Mesh Processing

  • Groups 140 labels into 17 anatomical categories

  • Creates separate OBJ files for each organ

  • Applies smoothing and mesh reduction

  • Supports detailed anatomical structures including:

    • Organs: Liver, Spleen, Pancreas, etc.

    • Skeletal system: Spine, Ribs, Shoulders, Hips

    • Vascular system: Veins and Arteries

    • Muscular system: Back muscles

Mesh to USD Conversion

  • Converts the processed meshes to USD format

  • Final USD files can be imported into Isaac Sim

NRRD to USD Converter Tool#

To convert NRRD medical images to USD format, follow these steps:

  1. Go to the i4h-workflows/tutorials/assets/CT_to_USD folder in the tutorials directory of Isaac for Healthcare.

  2. Install the required packages using the provided requirements.txt.

  3. Make a backup of your CT data, as the conversion will modify files in place.

  4. Run converter.py on your CT data folder to start the conversion process.

Usage#

Setup: Consider using a seperate virtual environment for this optional part of the course. If you have created a new environment for the MONAI workflow before, you can use this one.

conda activate monai
cd $I4H_HOME/tutorials/assets/CT_to_USD
pip install -r requirements.txt

Note

If you encounter issues with the additional dependencies, please use a seperate conda environment.

Usage: Copy your data to a sample folder of your choice, then export the folder name.

export GENERATED_DATA="/media/data/dli/maisi/sample_1/"

# Then run the converter
python utils/converter.py $GENERATED_DATA

In this video, we convert the previously generated CT data to a USD file and load it into IsaacS im.

Output Structure#

The converter generates:

output/
├── nii/           # Intermediate NIfTI files
├── obj/           # Intermediate mesh files  
└── all_organs.usd # Final USD file

Supported Anatomical Structures#

The tool processes 140 labels grouped into 17 categories including:

  • Organs: Liver, Spleen, Pancreas, Heart, Gallbladder, Stomach, Kidneys

  • Digestive: Small bowel, Colon

  • Skeletal: Spine, Ribs, Shoulders, Hips

  • Vascular: Veins and Arteries

  • Respiratory: Lungs

  • Muscular: Back muscles

Conversion Pipeline#

The tool implements the complete conversion workflow:

  1. NRRD → NIfTI: Format conversion for medical data

  2. NIfTI → Mesh: Surface extraction with smoothing and reduction

  3. Mesh → USD: Final format suitable for Isaac Sim and 3D visualization

Each organ maintains unique labeling for proper segmentation in the final USD file.

Load CT-derived Data Into Isaac Sim#

Open assets again#

  1. Launch Isaac Sim again.

  2. Find the path of your I4H-assets.

python -c "from i4h_asset_helper import get_i4h_local_asset_path; print(get_i4h_local_asset_path())"

  1. Open a CT-derived USD file, for example from i4h-workshop/outputs/. We provide some generated CT data, with the converted USD asset. You can downlaod it here.

Scene With Generated CT#

In this video, we build a new robotic ultrasound setup, with a patient model derived from the generated CT data.