Department of Radiology 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

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

BRAINS Tracer Visualization tool Tracing tool Landmark operations 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

BRAINSTracerQt

BRAINSTracer – Putamen Trace

BRAINSTracer – Talairach and Points

BRAINSTracer Other Features

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

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 –b workup.tcl

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

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 other images to the T1 weighted scan

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

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

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

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_AUTO directory Class plugs Continuous tissue classified Discrete tissue classified image

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 in 10_AUTO directory and intermediate results in ANN directory Label images for caudate, putamen, thalamus, hippocampus, globus pallidus

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

Surface Generation External Program Generate Genus Zero Surface 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

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

Surface Features

Surface Inflation

Surface Labeling

Command Line Programs Surface Visualization Registration 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