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Experiments with Predicting Landmarks in 3D MRI

As a little side project I wanted to predict four landmarks used to identify the EEG 10-10 system points. These four points include

  • Nasion (Nz)
  • Inion (Iz)
  • Left Pre-Auricular point (LPA)
  • Right Pre-Auricular point (RPA)

These points are visualized below: Nz (red), Iz (blue), LPA (green), and RPA (yellow).

front left back
front left back

Create Training Data

To create training data for this experiment I annotated 3 template datasets. Using our automatic head segmentation tool (head40), I segmented the template heads and 200 subjects from the Calgary-Campinas (CC) dataset. Grouping tissues I obtain simplified head labels:

  • brain (including CSF)
  • bone
  • air
  • spinal cord (including CSF)
  • other

base mask

Using SimpleITK I registered the template head labels to the CC dataset (affine and B-spline). By design the registration finds transforms that map from the moving (CC) to fixed (template) space. To transform the template landmarks to the CC space, we need to use the inverse transform. For each subject I now have 3 candidate positions for each landmark. To increase the accuracy and remove bias I average these three positions to create my training data for a RetinaNet.

Since I am using a box detector to locate 3D points, I simply create cubic boxes with fixed width (5mm) in cccwhd (X,Y,Z centers and width, height and depth).

Adapt MONAI Tutorial

For this purpose I adapted the detection tutorial from MONAI. That tutorial predicts lung nodules from CT images using RetinaNet. The things I needed to modify included

  • image normalization: instead of scaling from a fixed range to [0, 1] I use a NormalizeIntensityd transform.
  • since I want to learn left-right landmarks, I removed the random flip transforms
  • since the input data is MRI, I use different intensity augmentation, e.g.,
    • RandAdjustContrastd
    • RandHistogramShiftd
    • RandBiasFieldd
    • RandGibbsNoised
    • RandKSpaceSpikeNoised

Running the training for 300 steps takes 1-2 hours on my GPU (NVIDIA GeForce RTX 3090). I am not yet 100 percent familiar with the COCO metrics, but Recall IoU on the test data seems pretty good (considering the training data was generated automatically and not curated).

Nz AR IoU Iz AR IoU LPA AR IoU RPA AR IoU
0.85 0.87 0.89 0.91

Acknowledgement