NA-MIC National Alliance for Medical Image Computing Engineering a Segmentation Framework Marcel Prastawa.

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NA-MIC National Alliance for Medical Image Computing Engineering a Segmentation Framework Marcel Prastawa

National Alliance for Medical Image Computing Need for Segmentation Applications Longitudinal analysis of growth Preprocessing for shape analysis Detect pathology Fully automatic, reproducible Allow fast prototyping Execute on hundreds of datasets

National Alliance for Medical Image Computing Our Method: Atlas-based Brain Segmentation T1T2TissueCortex

National Alliance for Medical Image Computing Quick Demo

National Alliance for Medical Image Computing Engineering Components Filtering Inhomogeneity Correction Affine Registration Deformable Registration Segmentation Statistics Pathology Atlas

National Alliance for Medical Image Computing Shared Components (EMSegment) Filtering Registration Inhomogeneity Correction Statistics Atlas Pathology

National Alliance for Medical Image Computing Future Components New modality / information –DTI –Vessels / MRA Pathology model –Tumor biomechanical model –Lesion model New classifiers

National Alliance for Medical Image Computing GUI vs Batch Mode GUI for prototyping Command line for batch processing: –Use automatically generated XML file –Different input images, same parameters –Python or shell scripts

National Alliance for Medical Image Computing Sample XML Input [1/2] EMS /scratch/prastawa/atlases/adult-atlas RAI /scratch/prastawa/test/out GIPL /scratch/prastawa/test/T1_Orig.nrrd ASR /scratch/prastawa/test/T2_Orig.nrrd ASR...

National Alliance for Medical Image Computing Sample XML Input [2/2] Curvature flow

National Alliance for Medical Image Computing Smart Execution Fast prototyping by storing results at different stages Examples: –Store registration transforms –Store estimated intensity distributions Write new results when input parameters changed

National Alliance for Medical Image Computing Tumor Segmentation T13DT2 T13DT2

National Alliance for Medical Image Computing Neonate Segmentation T1T23D T1 T2 3D

National Alliance for Medical Image Computing Lupus Lesion Segmentation T2 FLAIR 3D

National Alliance for Medical Image Computing Discussion Integrated system for registration, bias correction, segmentation Implemented using ITK classes Cross-platform: Linux, Windows, Solaris Smart execution: stored states Shared components Slicer integration?