Airway Segmentation

OsiriX and Horos Course · Segmentation

In this video I show how to segment the airway from an MRI scan using OsiriX. The principle is similar to aortic segmentation, but “inverted”: instead of looking for a highly contrasted region, we look for a region with no density (air). Note: in MRI, the study often has few images (e.g., 32), which reduces the quality of the 3D. Even so, it is still possible to segment and obtain a useful model. Step by step (video workflow) 1) Select the “air” with Grow Region Open the study Go to ROI → Grow Region Click on an area of air and run Compute to select forward and backward If the selection comes out too large, I delete it and adjust: Delete All ROIs Reduce the selection range to better capture the low-density area In the video, I use values such as 20 and then 30 to improve the selection Compute again 2) Fix the small “holes” (Closing) After selecting the air, internal gaps usually appear: ROI → Brush ROIs → Closing Adjust the radius (in the video, I used 8 as a reference) This closes the holes and improves the airway outline. 3) Paint what is outside the ROI (negative value) To “clean up” the dataset: Select the option to apply to the ROIs Paint Outside ROIs with a negative value (it turns “black”, like air) Result: what is not of interest is visually “removed”. 4) Give high density to what is inside the ROI (positive value) Now I reinforce the airway as a solid structure: Paint Inside ROI with a high positive value (in the video: 1000) This makes the airway stand out clearly for the 3D. 5) Generate the 3D and remove the external air Open 3D Volume Rendering The 3D model appears (airway + external air) Use the scissors to erase what is external to the patient (air outside the head) Select → Delete You can rotate the 3D to check what is being cut Only the airway remains in 3D. How to calculate the airway volume (ROI Volume) Go back to the image window (sagittal/axial) Delete All ROIs to view only the “densified” airway Re-select with ROI → Grow Region → Compute (now it is fast because everything has uniform density) Go to ROI → ROI Volume and calculate In the example in the video, the calculated volume was 55 cm³.