1. Department of Radiology
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. 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

4. 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

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 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

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 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