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BRAINS Development

BRAINS Development. Vincent A. Magnotta Associate Professor Department of Radiology March 15, 2011. Acknowledgements. Hans Johnson Ronald Pierson Kent Williams Mark Scully Eun Young Kim Wen Li Steve Dunn Wei Lu. Design of Version 3. BRAINS Tracer. BRAINS Command Line.

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BRAINS Development

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  1. BRAINS Development Vincent A. Magnotta Associate Professor Department of Radiology March 15, 2011

  2. Acknowledgements • Hans Johnson • Ronald Pierson • Kent Williams • Mark Scully • Eun Young Kim • Wen Li • Steve Dunn • Wei Lu

  3. Design of Version 3 BRAINS Tracer BRAINS Command Line Command Line Programs – BRAINSFit, BRAINSCortex, etc GenerateCLP BRAINS - Library ITK VTK Qt TCL

  4. BRAINS Tracer • Visualization tool • Images, traces, landmarks, and surfaces • Generates surfaces from ROIs • Tracing tool • Now includes measurements • Landmark operations • GUI Interface for command line tools • Automated discovery of BRAINS tools • BRAINS TCL interface • Command line results sent to viewer

  5. BRAINSTracerQt

  6. BRAINSTracer – Putamen Trace

  7. BRAINSTracer – Talairach and Points

  8. BRAINSTracer Other Features

  9. BRAINS3 AutoWorkup • File format conversion • Spatial Alignment • Bias Field Correction and Normalization • Define Talairach Coordinate System • Tissue Classification • Neural Network • Volume Measurements • Surface Generation • Surface Measurements • Diffusion Tensor Analysis

  10. Running AutoWorkup • TCL Script required to run AutoWorkup • set baseDir /Users/vince/images/brainstestdata/trunk/MR/DICOM-GE-B2/TEST • set T1 $baseDir/T1_002 • set T2 $baseDir/T2_003 • set result [Brains::AutoWorkup::WorkupT1T2 $baseDir $T1 $T2] • Result is stored saved in baseDir/10_AUT0.Version • Execute script • brains3 –bworkup.tcl

  11. File Format Conversion • Convert DICOM images into NIFTI • BRAINSImageConversion • Results are saved in Stage0 directory within 10_AUTO directory

  12. Spatial Alignment • AC-PC alignment of T1 and T2 weighted images • BRAINSConstellationDetector • Automated detection of several landmarks including mid-sagittal plane, AC, PC, 4V, eyes • Run separately on each T1 and T2 weighted image • Results are saved in Stage1 directory within 10_AUTO directory • Aligned image • Landmarks • Transforms • Should register all otherimages to the T1 weighted scan

  13. Bias Field Correction • EM Segmentation • BRAINSABC • Performs discrete classification, image registration, bias field correction, brain extraction, and image averaging • B-Spline registration aligns atlas with subject • Final results are saved in 10_AUTO directory and intermediate results saved in BSITKBRAINSABC • Average T1 weighted image • Average T2 weighted image • Brain mask • Label image

  14. Image Normalization • TCL Script • Brains::WorkupUtils::StandardizeImageIntensity • Clips top and bottom 0.05% of histogram within the brain and scales to 0-255 for the T1 and T2 weighted images • Final results are saved in 10_AUTO directory • Normalized T1 weighted image • Normalized T2 weighted image

  15. Define Talairach Parameters • TCL Script and External Program • Brains::WorkupUtils::AutoTalairachParameters • BRAINSTalairach • Reads AC and PC points from the constellation detector program • Get bounding box from the brain mask • Final results are saved in 10_AUTO directory • Talairach parameter file • Talairach grid file

  16. Tissue Classification • TCL Script and External Program • Brains::WorkupUtils::PickBloodPlugsFromMargin • BRAINSClassPlugs • BRAINSClassify • Extract blood from edge of brain mask generated by BRAINSABC • Classic BRAINS tissue classification • Final results are saved in 10_AUTOdirectory • Class plugs • Continuous tissue classified • Discrete tissue classified image

  17. Neural Network Labeling • External Program • BRAINSCut • Align atlas to subject image using B-Spline registration and label based on T1 and T2 weighted images • Final results are saved in10_AUTO directory andintermediate results inANN directory • Label images for caudate,putamen, thalamus,hippocampus, globuspallidus

  18. Volume Measurements • External Program • Brains::Measure::ClassTalairachVolumes • BRAINSTalairachMask • Standard BRAINS Measurements based on tissue types • ANN Volumes • Final results are saved in 10_AUTO directory and intermediate results in Talairach directory • CSV file for ANN and Class Volumes • Talairach masks are in the Talairach directory

  19. Surface Generation • External Program • GenusZeroImageFilterOriginal • Generate Genus Zero Surface • Warp definitions of midline, brainstem and cerebellum to the subject (Diffeomorphic Demons) • Use definitions of caudate, putamen, thalamus and ventricles to fill in white matter • Low pass filter white matter image • Surface generation • Decimate and smooth surface • Final results are saved in 10_AUTO directory and intermediate results in Genus0 directory • Left and right surfaces

  20. Surface Labeling and Measurements • External Program • Register atlas surface with subject surface • Spherical diffeomorphic demons • Label surface using a Bayesian framework

  21. Surface Features

  22. Surface Inflation

  23. Surface Labeling

  24. Command Line Programs • Visualization • BRAINSTracerQt – Visualization and Tracer for BRAINS • Registration • BRAINSFit – Rigid and affine registration • BRAINSDemonsWarp – Non-rigid registration • BRAINSConstellationDetector – ACPC finder • Tissue Classification • BRAINSABC -Tissue classification / bias field correction module • BRAINSKmeansClusterSamples – K-means classification • BayesianClassifier – Bayesian classification • BRAINSClassPlugs – Plug estimation • BRAINSClassify – Multi-modal tissue classification • BRAINSDiscreteClass – Continuous to discrete conversion • Labeling • BRAINSMush – Brain mask creation • BRAINSTalairach – Create Talaiarch Parameters and atlas based binary images • BRAINSCut – Automated labeler • BRAINSTalairachMask – Create a Talairach mask based on atlas definition • Surface • BRAINSCortex – Surface generation • GenusZeroFilterOriginal – Surface topology correction • Difusion Tensor Imaging • GTRACT – Diffusion Tensor Imaging

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