BRAINS Development

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