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Convert3D::Advanced

Advanced Convert3D and ITK-SNAP Examples

This page will contain worked examples of using ITK-SNAP and C3D to perform complex tasks.

Interpolating segmentations

In this example, we create a rough segmentation of a 3D object by quickly labeling a few slices along one plane in ITK-SNAP and then using C3D to extrapolate the shape in between the drawn slices. This is useful for creating registration masks, initializing registration, etc.

Rough segmentation in ITK-SNAP

In this example we work with a postmortem hippocampus MRI scan. Labeling the whole hippocampus in this scan could take hours, and we just want a rough segmentation. So we go into ITK-SNAP and use the polygon tool to label a dozen or so slices. They do not have to be at regular intervals, as seen below.

Attach:sliceseg.png Δ

Interpolation in C3D

We perform interpolation in two stages. First, we use a distance transform with some smoothing to generate a rough 3D interpolation (which might be already good enough for some applications).

Page last modified on April 29, 2015, at 09:21 AM

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