Added segmentation on oblique slices

lassoan · Apr 4, 2019 · babf116 · babf116
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diff --git a/Craniotomy/README.md b/Craniotomy/README.md
@@ -8,7 +8,7 @@ Overview
 Prerequisites
 -------------
 
-Have a segment that need to cut/partitioned into multiple pieces
+Have a segment that need to be cut/partitioned into multiple pieces.
 
 Recommended workflow
 --------------------

diff --git a/ObliqueSliceSegmentation/AdjustLabelmapResolution.png b/ObliqueSliceSegmentation/AdjustLabelmapResolution.png
diff --git a/ObliqueSliceSegmentation/CreateRotatedROI.png b/ObliqueSliceSegmentation/CreateRotatedROI.png
diff --git a/ObliqueSliceSegmentation/CropVolumeWithRotatedROI.png b/ObliqueSliceSegmentation/CropVolumeWithRotatedROI.png
diff --git a/ObliqueSliceSegmentation/MisalignmentWarningButton.png b/ObliqueSliceSegmentation/MisalignmentWarningButton.png
diff --git a/ObliqueSliceSegmentation/README.md b/ObliqueSliceSegmentation/README.md
@@ -0,0 +1,51 @@
+Overview
+--------
+
+- Task: Segment image on slices that are not aligned with axes of the master volume.
+- Imaging modality: any 3D imaging modality (CT, MRI, ...)
+
+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](SliceViewAxesAligned.png)
+
+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](SliceViewAxesNotAligned.png)
+
+![Slice view axes not aligned with segmentation axes](SliceViewAxesNotAlignedExample.png)
+
+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](MisalignmentWarningButton.png)
+
+Recommended workflow
+--------------------
+
+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](AdjustLabelmapResolution.png)
+
+![Due to higher resolution, stripe artifacts do not appear anymore](SliceViewAxesNotAlignedExampleOvesampled.png)
+
+### Option B. Create resampled volume with rotated axes
+
+- Define a region of interest (ROI) by selecting ROI from the dropdown menu of the place button on toolbar.
+- Apply rotation transform to the ROI and adjust rotation sliders (or use any precomputed transforms, such as inverse of volume's AC-PC transform)
+
+![Create ROI that has axes aligned with the desired orientation](CreateRotatedROI.png)
+
+- Use `Crop volume` module to crop the volume with the ROI
+
+![Crop volume with rotated ROI](CropVolumeWithRotatedROI.png)
+
+- Use the cropped volume as Master volume in the Segment Editor
+
+![Segment resampled volume](SegmentOnCroppedROI.png)
diff --git a/ObliqueSliceSegmentation/SegmentOnCroppedROI.png b/ObliqueSliceSegmentation/SegmentOnCroppedROI.png
diff --git a/ObliqueSliceSegmentation/SliceViewAxesAligned.png b/ObliqueSliceSegmentation/SliceViewAxesAligned.png
diff --git a/ObliqueSliceSegmentation/SliceViewAxesNotAligned.png b/ObliqueSliceSegmentation/SliceViewAxesNotAligned.png
diff --git a/ObliqueSliceSegmentation/SliceViewAxesNotAlignedExample.png b/ObliqueSliceSegmentation/SliceViewAxesNotAlignedExample.png
diff --git a/ObliqueSliceSegmentation/SliceViewAxesNotAlignedExampleOvesampled.png b/ObliqueSliceSegmentation/SliceViewAxesNotAlignedExampleOvesampled.png
diff --git a/README.md b/README.md
@@ -5,6 +5,7 @@ Recipes for solving common segmentation tasks using 3D Slicer
 - [Craniotomy (splitting segments)](Craniotomy/README.md)
 - [Aorta segmentation (fast, using Fast marching)](AortaFastMarching/README.md)
 - [Aorta segmentation (high-accuracy, using Grow from seeds)](AortaMaskedGrowFromSeeds/README.md)
+- [Segmentation on arbitrarily oriented slices](ObliqueSliceSegmentation/README.md)
 
 External links:
 - Whole heart segmentation from CTA: