Foundation_model.md

MedSAM2 Integration and Slice Propagation for Brain MRI Segmentation in 3D Slicer

1. 3D Slicer Setup

• Install the latest version of [https://www.slicer.org/](3D Slicer).
• Load2-5 brain MRIs (BraTS is a good choice).

2. MedSAM2 Integration

• Python Interactor in Slicer to call the MedSAM2 model.
• Or write a simple scripted module wrapping MedSAM2 inference.

3. Slice Propagation Practice

• Pick a few slices and run MedSAM2 (e.g., bounding box or point prompt). Adjust the settings to achieve the best performance possible.
• Then, manually or semi-automatically propagate the segmentation to neighboring slices using:
  • 3D Slicer’s built-in “fill between slices” tool in Segment Editor
  • Or simulate your own logic using simple interpolation

4. Evaluation

• Compare your mask against the ground truth mask using Dice Similarity Coefficient (DSC)
• Document any challenges or observations (e.g., drift, oversegmentation).

5. Deliverables

• Screenshots or screen recordings showing segmentation + propagation
• Code or scripts used
• Short report explaining:
  • Workflow
  • How propagation was tested
  • Quantitative results + interpretation
  • Any limitations or ideas for improvement