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SlicerSegmentationRecipes

Recipes for solving common segmentation tasks using 3D Slicer

Overview

Segment Editor allows editing of segmentation on slices of arbitrary orientation. However, since edited segments are stored as binary labelmaps, “striping” artifacts may appear on thin segments or near boundary of any segments.

When slice view axes are aligned with segment axes: segment boundaries may appear “blocky” in slice views, but no other artifacts appear.

Slice view axes aligned with segmentation axes

When slice view axes are not aligned with segment axes: slice view is filled from voxels of several planes of the segmentation, therefore the thin objects or boundary of a solid object may appear to have a striped pattern.

Slice view axes aligned with segmentation axes

Slice view axes not aligned with segmentation axes

Slicer notifies the user if slice view axes are not aligned with segment axes by showing a warning icon in the Segment Editor, next to the segmentation node selector. If the warning button is clicked, each slice view is automatically aligned to the closest segment axis.

Warning icon appears if slice view axes are not aligned with segmentation axes

Depending on what is the end goal, there are several approaches to deal with stripe artifacts.

Option A. Ignore stripes

Stripe artifacts can be safely ignored. Correctness of the segmentation near object boundaries can be verified by enabling slice view intersections and reviewing multiple neighboring slices.

Probability of seeing stripe artifacts can be greatly reduced by making the segmentation resolution finer. This can be achieved by oversampling the segmentation.

Labelmap resolution is increased by oversampling

Due to higher resolution, stripe artifacts do not appear anymore

Option B. Create resampled volume with rotated axes

Create ROI that has axes aligned with the desired orientation

Crop volume with rotated ROI

Segment resampled volume