Automated MRI Segmentation and Analysis Framework (AMSAF)
https://www.gitbook.com/book/iancmcdonald/amsaf/details
Further documentation contained here:Meta:
Goal: Automate the generation and testing of MRI segmentations
**High-level implementation: **Grid search over the Elastix parameter space, constrained by our prior intuition and experience.
Tools: Python, Elastix, SimpleElastix
Thoughts to keep in mind:
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Time constraints
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Each registration + segmentation takes a few minutes to complete
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Space constraints:
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Each image takes up a significant amount of space, sometimes up to 500MB
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Modularity:
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As this project evolves, we may replace components of this framework to fit new insights or tools. For instance, we should not write this in such a way that we could easily replace Elastix for another registration framework like ANTs
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Each piece is sufficiently complex so as to warrant component-level unit testing
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Abstraction and ease of use:
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People years from now might want to use this, so write with them in mind
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Abstract away low-level implementation details without sacrificing results
High-Level Components:
Segmenter
- Purpose: Automatically Segment MRI images
- Implementation: Registration-based segmentation parameterized by target and manually segmented reference images. This should be flexible enough to accommodate switching out registration tools and frameworks while keeping the code altering to a minimum.
Segmentation Evaluator
- Purpose: Evaluate segmentation results
- Implementation: Image subtraction or DICE similarity
Linker
- Purpose: Link individual components
Executor
- Set Linker values and execute segmentation
Component Tester
- Purpose: Test other framework components