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quanghieu31/lumbar-spine-degenerative-classification

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Goal

  • Detect and classify lumbar degenarative spine (LSD) conditions using lumbar sping MR images
  • More information, credits, and data are on the Kaggle competition website.

The 5 conditions are

  • Left Neural Foraminal Narrowing
  • Right Neural Foraminal Narrowing
  • Left Subarticular Stenosis
  • Right Subarticular Stenosis
  • Spinal Canal Stenosis

For each condition, classify the 5 intervertebral disc levels (IDL) = location of the compression

  • L1/L2
  • L2/L3
  • L3/L4
  • L4/L5
  • L5/S1

Classify how severe of compression of the spinal cord due to foramina/subarticular exit (severity score/level) weights

  • Normal/mild = 1
  • Moderate = 2
  • Severe = 4

So, essentially, for each observation, we have 5*5=25 output variables, each of which needs to be classified as one of the 3 severity levels.

Steps:

  1. Conduct EDA to understand the data and distributions: rsna-lumbar-eda.ipynb
  2. Develop essential functions to deal with data like making metadata, showing images, and coordinating directories: rsna-lumbar-keyfunctions.ipynb
  3. Examine the coordination of pathology and look into several images given the previously built functions: rsna-lumbar-imageprocessing-and-coordpathology.ipynb
  4. Convert the DICOM images into PNG for convenience and select subsets of the images for training: rsna-making-dataset-png.ipynb
  5. Make Dataset, DataLoader, transformations, define a ResNet50 model and training loop on AdamW optimizer and cuda GPU T4x2: rsna-training-resnet50-gpu.ipynb. I will add more details to this. I had such a great time to learn from other notebooks on how to handle the data/image processing problem that involves multiple outcome variables for 3-class classification.

Some visual info:

  • Left Neural Foraminal Narrowing
  • Right Neural Foraminal Narrowing
5 intervertebral disc levels Severity
  • Left Subarticular Stenosis
  • Right Subarticular Stenosis
5 intervertebral disc levels Severity
  • Spinal Canal Stenosis
5 intervertebral disc levels Severity

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Code for a kaggle competition in neuroradiology

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