3D Slicer Tutorial
3D Echocardiography

March 17, 2026 – We are pleased to share a new addition to the NeoCardioLab website featuring the work of Ellory Morro, student at NeoCardioLab, who has developed an innovative approach to estimating left ventricular volumes in newborns using 3D echocardiography. In this project, Ellory worked with 3D echo datasets to perform detailed segmentation of cardiac volumes and explored methods to derive simplified, clinically applicable volume estimates. Her work demonstrated that the most accurate approximation of true 3D left ventricular volume can be achieved using a mathematical model based on three key measurements obtained directly from the 3D echocardiographic acquisition (manuscript in production). To support knowledge translation and reproducibility, Ellory has created a comprehensive step-by-step video tutorial outlining the segmentation process, the methodological framework, and the derivation of the model. In addition, an interactive calculator is now available within this section to facilitate rapid estimation of left ventricular volumes using this approach. This new resource aims to bridge advanced imaging analysis with practical bedside application and reflects our ongoing commitment to developing accessible, physiology-driven tools for neonatal hemodynamic assessment.

This video tutoral was uploaded on March 17, 2026 and created on March 15, 2025. This video was created by Ellory Morro, student at NeoCardioLab (www.neocardiolab.com ). It presents a study on 3D segmentation of cardiac volumes using the open-source image computing platform 3D Slicer. The video serves as a step-by-step tutorial demonstrating the segmentation workflow and highlighting the practical application of 3D Slicer for cardiac image analysis.

3D Segmentation of the Left Ventricle in Newborns Using 3D Slicer

Below, we provide a comprehensive guide on utilizing the 3D Slicer image computing platform to derive a three-dimensional segmentation model of the left ventricle (LV) from 3D echocardiogram data. This process is essential for detailed anatomical analysis and precise volume approximations in neonatal cardiology.

Prerequisites and Preparation

Before beginning the segmentation process, ensure your data and software are correctly configured:

• Data Format: The 3D echocardiogram must be converted into a 3D Cartesian map and saved in DICOM format.

• File Organization: Organize files into a patient-specific folder. Labeling files with the patient’s name and ID is critical, as the software's internal directory may not display file contents during selection.

• Extensions: Install necessary extensions via the Installation Manager. Key extensions include Slicer Heart, which is required for cardiac-specific data processing.

Step-by-Step Tutorial

Step 1: Patching the DICOM Data

The raw ultrasound data often requires "patching" to be fully compatible with 3D Slicer's analysis tools.

1. Navigate to the Cardiac module and select the Philips 4D US DICOM patcher.

2. Set the Input DICOM directory to the folder containing your 3D Cartesian DICOM files.

3. Select a new folder for the Output directory, labeling it "patched" to distinguish it from raw data.

4. Run the process; a notification will appear at the bottom of the screen once patching is complete.

Step 2: Importing and Loading Data

1. Click the DICOM import button and select your "patched" files.

2. Once the database loads, select the relevant patient files and click Load to bring them into the 3D Slicer workspace.

3. On the left-hand panel, scroll through the available ultrasound images to select the highest-quality view for your model.

Step 3: Initializing the Segment Editor

1. Open the Segment Editor module.

2. Critical Step: Ensure the Source Volume in the drop-down menu matches the specific ultrasound image number you selected in the viewer.

3. Click Add a Segment once you have a clear view of the left ventricle in all three axes.

Step 4: Manual Segmentation (Painting)

1. Select the Paint feature.

2. Adjust Brush Diameter: Use a wider brush for filling the center of the ventricle and a finer brush for capturing the intricate borders of the ventricle wall.

3. Multi-Axis Editing: Utilize the 3D view in the top-right corner to monitor the brush's position across all three dimensions.

4. Frame-by-Frame Modeling: Start with a central image, outlining the exterior and filling the interior. It is recommended to fill a segment approximately every four to five frames; the software will assist in connecting these segments.

5. Toggle Show 3D on the left panel to visualize the model as it develops.

Step 5: Refining the Model

Once the rough segmentation is complete, you must smooth the "hatched" product to create a realistic anatomical model.

1. Navigate to the Smooth setting.

2. Select Joint Smoothing from the available options.

3. Set the Smoothing Factor to 0.5.

4. Under smoothing brush options, select the lowest percentage (1%) to preserve the finer intricacies of the ventricle wall.

Step 6: Extracting Statistics and Linear Measurements

1. Go to the Data module, right-click your segmentation, and select Segment Statistics.

2. Confirm the source ultrasound number is consistent with your editing.

3. Select the desired features (e.g., voxel count, volume, roundness) and click Apply to generate a statistics table.

4. For manual linear measurements, use the Markups tool.

5. Place points to measure three specific axes: top-down (longitudinal), left-to-right (transverse), and anterior-posterior.

Step 7: Data Export and Volume Calculation

1. Save the Scene: Save the "Scene View" to allow for future editing, ensuring only the active ultrasound volume is selected.

2. Export Tables: Save your statistics and measurement tables in CSV format for use in external software like Excel.

3. Volume Approximation: Input your manual linear measurements into a volume approximation spreadsheet. These formulas will calculate the area of the ellipse and provide the final volume in cubic millimeters (mm³) and milliliters (mL).