NA-MIC National Alliance for Medical Image Computing Engineering a Segmentation Framework Marcel...
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NA-MICNational Alliance for Medical Image Computing http://na-mic.org
Engineering a Segmentation Framework
Marcel Prastawa
National Alliance for Medical Image Computing http://na-mic.org
Need for Segmentation Applications
• Longitudinal analysis of growth• Preprocessing for shape analysis• Detect pathology
Fully automatic, reproducibleAllow fast prototypingExecute on hundreds of datasets
National Alliance for Medical Image Computing http://na-mic.org
Our Method: Atlas-based Brain Segmentation
T1 T2 Tissue Cortex
National Alliance for Medical Image Computing http://na-mic.org
Quick Demo
National Alliance for Medical Image Computing http://na-mic.org
Engineering ComponentsFiltering
Inhomogeneity Correction
Affine Registration
Deformable Registration
Segmentation
Statistics
Pathology
Atlas
National Alliance for Medical Image Computing http://na-mic.org
Shared Components (EMSegment)
• Filtering• Registration• Inhomogeneity Correction• Statistics
• Atlas• Pathology
National Alliance for Medical Image Computing http://na-mic.org
Future Components
• New modality / information– DTI– Vessels / MRA
• Pathology model– Tumor biomechanical model– Lesion model
• New classifiers
National Alliance for Medical Image Computing http://na-mic.org
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 http://na-mic.org
Sample XML Input [1/2]<?xml version="1.0"?><!DOCTYPE SEGMENTATION-PARAMETERS><SEGMENTATION-PARAMETERS><SUFFIX>EMS</SUFFIX><ATLAS-DIRECTORY>/scratch/prastawa/atlases/adult-atlas</ATLAS-
DIRECTORY><ATLAS-ORIENTATION>RAI</ATLAS-ORIENTATION><OUTPUT-DIRECTORY>/scratch/prastawa/test/out</OUTPUT-DIRECTORY><OUTPUT-FORMAT>GIPL</OUTPUT-FORMAT><IMAGE> <FILE>/scratch/prastawa/test/T1_Orig.nrrd</FILE> <ORIENTATION>ASR</ORIENTATION></IMAGE><IMAGE> <FILE>/scratch/prastawa/test/T2_Orig.nrrd</FILE> <ORIENTATION>ASR</ORIENTATION></IMAGE>...
National Alliance for Medical Image Computing http://na-mic.org
Sample XML Input [2/2]...<FILTER-ITERATIONS>1</FILTER-ITERATIONS><FILTER-TIME-STEP>0.01</FILTER-TIME-STEP><FILTER-METHOD>Curvature flow</FILTER-METHOD><MAX-BIAS-DEGREE>4</MAX-BIAS-DEGREE><PRIOR-1>1.2</PRIOR-1><PRIOR-2>1</PRIOR-2><PRIOR-3>0.7</PRIOR-3><PRIOR-4>1</PRIOR-4><DO-ATLAS-WARP>1</DO-ATLAS-WARP><ATLAS-WARP-GRID-X>5</ATLAS-WARP-GRID-X><ATLAS-WARP-GRID-Y>5</ATLAS-WARP-GRID-Y><ATLAS-WARP-GRID-Z>5</ATLAS-WARP-GRID-Z></SEGMENTATION-PARAMETERS>
National Alliance for Medical Image Computing http://na-mic.org
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 http://na-mic.org
Tumor Segmentation
T1 3DT2
T1 3DT2
National Alliance for Medical Image Computing http://na-mic.org
Neonate Segmentation
T1 T2 3D
T1 T2 3D
National Alliance for Medical Image Computing http://na-mic.org
Lupus Lesion Segmentation
T2 FLAIR
3D
National Alliance for Medical Image Computing http://na-mic.org
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?