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

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Presentation on theme: "BRAINS Development Vincent A. Magnotta Associate Professor Department of Radiology March 15, 2011."— Presentation transcript:

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

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 –b workup.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 other images 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 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_AUTO directory – 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 in 10_AUTO directory and intermediate results in ANN directory – Label images for caudate, putamen, thalamus, hippocampus, globus pallidus

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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