Software at CIS : ITK and VTK modules for shape analysis

ITK and VTK Module Contributions

Slicer3D Visualization

Child and Adolescent Templates

Group

Number of subjects

Mean Age

Age STD

Sex

byu

vtk

MDD Left Hippo

10

9.04

0.81

F

MDD_Left.byu

MDD_Left.vtk

MDD Right Hippo

12

8.88

0.83

F

MDD_Right.byu

MDD_Right.vtk

Control+MDD Left Hippo

22

8.89

0.75

F

Control_MDD_Left.byu

Control_MDD_Left.vtk

Control+MDD Right Hippo

26

8.85

0.75

F

Control_MDD_Right.byu

Control_MDD_Right.vtk

Control Left Hippo

13

8.76

0.68

F

Control_Left.byu

Control_Left.vtk

Control Right Hippo

15

8.82

0.69

F

Control_Right.byu

Control_Right.vtk



Age Group

Structure

Side

Subjects

Patients

Mean Age

Age STD

Male

Female

Data

4 to 5

Amygdala Core

Left

2

2

5.33

0.73

1

1

Data

4 to 5

Amygdala Core

Right

2

2

5.33

0.73

1

1

Data

4 to 5

Amygdala Noncore

Left

2

2

5.33

0.73

1

1

Data

4 to 5

Amygdala Noncore

Right

2

2

5.33

0.73

1

1

Data

4 to 5

Hippocampus

Left

2

2

5.33

0.73

1

1

Data

4 to 5

Hippocampus

Right

2

2

5.33

0.73

1

1

Data

6 to 9

Amygdala Core

Left

8

6

8.52

0.93

4

4

Data

6 to 9

Amygdala Core

Right

7

5

8.61

1.04

4

3

Data

6 to 9

Amygdala Noncore

Left

8

6

8.52

0.93

4

4

Data

6 to 9

Amygdala Noncore

Right

7

5

8.61

1.04

4

3

Data

6 to 9

Hippocampus

Left

8

6

8.52

0.93

4

4

Data

6 to 9

Hippocampus

Right

7

5

8.61

1.04

4

3

Data

10 to 15

Amygdala Core

Left

2

2

13.08

1.65

1

1

Data

10 to 15

Amygdala Core

Right

3

2

12.2

1.89

1

2

Data

10 to 15

Amygdala Noncore

Left

2

2

13.08

1.65

1

1

Data

10 to 15

Amygdala Noncore

Right

3

2

12.2

1.89

1

2

Data

10 to 15

Hippocampus

Left

2

2

13.08

1.65

1

1

Data

10 to 15

Hippocampus

Right

3

2

12.2

1.89

1

2

Data

15 and up

Hippocampus

Left

4

2

18.4

1.22

3

1

Data

15 and up

Hippocampus

Right

3

2

18.2

1.41

3

0

Data

Visualization

  • To visualize the first N Laplace-Beltrami surface harmonics of a template.

    The CIS Laplace-Beltrami filter is available from the itk git repository, on the LaplaceBeltramiOperator topic branch. For instructions on how to check out this branch of the repository, see

    http://www.itk.org/Wiki/ITK/Git/Develop

    Once you've checked out and built the code, under "bin" in your build directory, locate the program LaplaceBeltramiOperator. Run: 
    bin/LaplaceBeltramiOperator 13 your_population_template.byu
    to create the first 13 surface harmonics on the template.

    To visualize, use CAWorks/ParaView:
    1. Go to 3D view.
    2. File->Open
    3. Select SurfaceHarmonic_..vtk
    4. Click OK
    5. In the "Time" text box, enter "1"
    6. In the Object Inspector, Display tab, click Rescale to Data Range
    7. View->Animation View
    8. In Animation View - Mode: Real Time
    9. Press play button
  • To visualize the population to template momenta

    Given a set of vtkPolyData files (alpha0_*.vtk) with the momenta defined as PointData set PointColorMomentumData, visualize momenta in Paraview/CAWorks:

    1. paraview/caworks2
    2. File->Open
    3. Select Momenta File (one of the *.vtk)
    4. In "Object Inspector" panel, Display tab, Color Section, click "Color By" combo box and select PointColorMomentumData
  • To create the Principle Components of population to template momenta

    The CIS Kernel PCA operator is available from the itk git repository, on the KernelPCAOnMeshes topic branch. For instructions on how to check out this branch of the repository, see

    http://www.itk.org/Wiki/ITK/Git/Develop

    Once you've checked out and built the code, under “bin” in your build directory, locate the program VectorKernelPCA. Given a set of vtkPolyData files (alpha0_*.vtk) with the momenta defined as PointData set PointColorMomentumData, run: 
    bin/VectorKernelPCA 11 6.5 your_template_file PCA_Computations_ alpha0_*.vtk
    to create the first 11 Principal Components of the template to population momenta. The Kernel sigma used here is 6.5 which is standard for most anatomical structures, but be sure to enter the kernel sigma you used to calculate the momentum data.

  • To visualize the Principle Components of population to template momenta in CAWorks/Paraview
    1. caworks2/paraview
    2. File->Open
    3. Select a PCA file (PCA_ComputationsBasis*.vtk)
    4. In "Object Inspector" panel, Display tab, Color Section, click Color By combo box and select PointColorMomentumData.
  • To visualize the Principle Components of population to template momenta in Slicer3D

    This grant required the creation of a software library, compatible with Paraview/CAWorks, that is capable of writing the objects loaded into ParaView/CAWorks into a SceneGraph in MRML format which can be loaded into Slicer3D.

    1. Create the SceneGraph:
      1. caworks2
      2. File-<Open
      3. Select a PCA file(s) (PCA_ComputationsBasis*.vtk)
      4. File->Save into a KWScene
    2. Create the SceneGraph
      1. slicer3d
      2. File->Add File->Choose File(s) to Add->browse to file from step iv.
      3. View->Layout->3D Only
      4. Module View Controllers->3D View Controllers->Center the 3D view on the scene"
      5. Module Models -> Scene -> Hilight PCA_Computation Basis
      6. Display Tab -> Scalars Tab -> Check Visible and set Active Scalar to PointColorMomentumData

 

Last Modified: Wednesday, 22nd May, 2013 @ 04:11pm