Orient and Resize
> Open "C:/Temp/A.mhd#SS3"
> Orient Given="RPI" Desired="ASL"
> Properties Origin=itkPoint(0,0,0)
> Save "C:/Temp/A-ASL.mhd"
> CastToF
> Resize OutputSize=itkSize(256,256,256) Interpolator="Linear"
> Save "C:/Temp/A-ASL-SMALL.mhd"
> Close

Speed Function
> Open "C:/Temp/A-ASL-SMALL.mhd#F3"
> CurvatureFlow TimeStep=0.1 Iterations=10
> Threshold Lower=-2000 Upper=100 OutsideValue=100
> ConnectedThreshold Lower=60 Upper=100
Seed=[50, 90, 100]
> Rename "Sternum"
> BinaryPixelMath Operation="Add" Input1="Threshold" Input2="Sternum"
> LevelSetSpeed OutputMinimum=0.0
Gaussian Normalize=False
Gaussian Sigma=0.5
Sigmoid Alpha=-10.0
Sigmoid Beta=10.0
Threshold Lower=-250.0
Threshold Upper=355.0
Rescale OutputMinimum=000.000
Rescale OutputMaximum=001.000
> Save "C:/Temp/A-ASL-SMALL-SPEED.mhd"
> Close

Initial Contour
> Open "C:/Temp/A-ASL-SMALL.mhd#SS3"
> BinaryThreshold Lower=-250 Upper=2000
> CastToUC
> GenerateMaskFromFile "C:/Temp/A-SPHERES.txt"
> BinaryPixelMath Operation="Mask" Input1="Cast" Input2="Mask"
> MorphologicalOpen Operation="Binary" KernelRadius=itkSize(4,4,4)
> Save "C:/Temp/A-ASL-SMALL-INITIAL.mhd"
> Close

Fast Marching
> Open "C:/Temp/A-ASL-SMALL.mhd#SS3"
> Open "C:/Temp/A-ASL-SMALL-INITIAL.mhd#UC3"
> Open "C:/Temp/A-ASL-SMALL-SPEED.mhd#F3"
> FastMarching InitialImage="Initial" StoppingValue=100.0
> MorphologicalErode KernelRadius=itkSize(2,2,2)
> BinaryThreshold Lower=0 Upper=14
> CastToUC
> Resize OutputSize=itkSize(512,373,512) Interpolator="Nearest"
> Save "C:/Temp/A-ASL-HEART.mhd"
> Close

Vesselness
> Open "C:/Temp/A-ASL-SMALL.mhd#F3"
> Vesselness Sigma=0.7
> ImageRange Minimum=0.0 Maximum=100.0
> ConnectedThreshold Lower=40 Upper=1000
Seed=[95, 122, 169]
Seed=[126, 86, 96]
> CastToUC
> Resize OutputSize=itkSize(512,373,512) Interpolator="Nearest"
> MorphologicalDilate Operation="Binary" KernelRadius=itkSize(2,2,2)
> Save "C:/Temp/A-ASL-VESSELS.mhd"
> Close

Combine Tags
> Open "C:/Temp/A-ASL-VESSELS.mhd#UC3"
> Open "C:/Temp/A-ASL-HEART.mhd#UC3"
> ShiftScale Shift=-150
> BinaryPixelMath Operation="Max" Input1="Heart_Shift" Input2="Vessels"
> Save "C:/Temp/A-ASL-TAGS.mhd"
> Close

Histogram
> Open "C:/Temp/A-ASL-SMALL.mhd#F3"
> MorphologicalGradientMagnitude KernelRadius=itkSize(1,1,1)
> ValueEdgeHistogram Value="Small" Edge="Magnitude" NumberOfBins=[512,128]
> Save "C:/Temp/A-ASL-HISTOGRAM.png"
> Close

Volume Render
> Open "C:/Temp/A-ASL-HISTOGRAM.png#UC2"
> Open "C:/Temp/A-ASL-TAGS.mhd#UC3"
> Open "C:/Temp/A-ASL.mhd#SS3"
> MorphologicalGradientMagnitude KernelRadius=itkSize(1,1,1)
> RescaleIntensityToUC
> VolumeRender Value="A-ASL.mhd" Gradient="Rescale" Tags="Tags"
        Tf=siTransferFunction(itkSize(512,128),"All","Heart","Vessels")