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NA-MIC / ProjectWeek

Website for NA-MIC Project Weeks
https://projectweek.na-mic.org
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Project: Brain Tumor segmentation with Missing Data #1206

Closed ReubenDo closed 3 months ago

ReubenDo commented 3 months ago

Draft Status

Ready - team will start page creating immediately

Category

Segmentation / Classification / Landmarking

Presenter Location

In-person

Key Investigators

Project Description

This project aims to create a Slicer extension that can automatically segment brain tumors in brain multi-parametric MRI, even in the presence of missing data.

This project will focus on two use cases where:

The algorithm will not only segment the scans but also perform the required pre-processing steps (co-registration and skull-stripping).

Objective

  1. Develop a Slicer module that can automatically perform brain tumor segmentation
  2. Create a module that has the flexibility to handle two potential sets of input data
  3. Integrate pre-processing steps for end-to-end inference
  4. Validate the module with a subset of BraTS and clinical data

Approach and Plan

  1. Train two combinations of nnUnet using the BraTS dataset.
  2. Integrate the pre-trained nnUnet frameworks into Slicer using the TotalSegmentator Slicer plugin as a template
  3. Leverage Slicer tools to perform the BraTS preprocessing steps
  4. Collect clinical data for validation

Progress and Next Steps

No response

Illustrations

image

Background and References

No response

github-actions[bot] commented 3 months ago

Project Page Pull Request Creation

:white_check_mark: COMPLETED: See https://github.com/NA-MIC/ProjectWeek/pull/1208