baiti01/curve-gcn-cardiac-mr

Curve-GCN for Cardiac MRI Segmentation

These are some preliminary results on applying Curve-GCN (https://arxiv.org/abs/1903.06874) to the problem of cardiac MRI segmentation.

Unlike commonly used neural networks for image segmentation (FCN, U-net), Curve-GCN predicts contour points around an object's boundary similar to how humans annotate images.

For this specific application, I extended the network to perform segmentation of upto 3 objects: left ventricle (LV), myocardium (Myo) and right ventricle (RV). Also, since some images only have 1 or 2 of these structures, I added an additional head to classify whether the image contains each structure or not.

A diagram of the network architecture is shown below.

I used the polygon loss for predicting the contour loss and a binary cross-entropy loss for the additional classification branch.

Results

Representative results are shown below. While the LV segmentation performance is comparable to U-net performance, Myo and RV segmentation performance are worse than the U-net.

Interesting Points

• There is a jump from image or feature maps to coordinates. Using something like CoordConv (https://arxiv.org/abs/1807.03247) might help.

• We are only using a small fraction of pixels in each image/feature map.

Improving Curve-GCN Results

• Add constraints on curvature of polygon

• Add IOU/Dice loss

• Add domain specific knowledge:

  • Red contour must be inside blue contour
  • Green contour shares border with blue contour on most slices

• Sampling and GNN are not equivariant to translation

• More data

Note

Note that due to the original Curve-GCN code's license, a lot of the code was redacted here. Please send me an email at [email protected] if you would like to learn more about this project.