New Users

If this is the first time you have visited this web page, the Introduction section below would be a good place to start.

• Clinical
• Background
• BIRN PORTAL
• Introduction
• Login
• LDDMM BIRN Portal
• Select Dimension
• Select Browse
• Select Atlas Image
• Select Target Image
• Select Output
• Launch processing
• View Status Menu
• Visualize Data
• InQ
• InQ lddmm directory
• Get Data through Scommands
• Visualize using MayaVi
• Visualize using ParaView

DATA

• BIRN Hippocampus Input data (1.1M)
• BIRN Hippocampus Output data (42MB)

Introduction

The lddmm BIRN Portal is being developed to enhance the lddmm processing and analysis of image data. This tutorial is aimed at persons wishing to analyze shape data using lddmm.

Under the auspices of the Brain Morphometry Biomedical Informatics Research Network (mBIRN), a processing pipeline (SASHA - Semi-Automated Shape Analysis) is being developed to enable seamless processing of brain morphometry data for subcortical structures through the integration of multiple site applications The components of SASHA are:

LDDMM - software that allows for comparison and quantization of morphometric changes in shapes.

Free Surfer - set of semi-automated tools for reconstruction of the brain's cortical surface and overlay of functional data onto the reconstructed surface.

3D Slicer - open-source application that assists with the visualization, registration, segmentation, and quantification of medical image data.

This tutorial covers use of lddmm on the BIRN Portal and viewing the results. At the end of the tutorial a user will be able to run lddmm on the BIRN Portal and visualize the results. In the tutorial the user will access the LDDMM BIRN portal, select two hippocampus volumes to compare, Run lddmm and visualize the output. For further information on lddmm refer to Clinical Background.

This can require large computational resources, depending on the images used for comparison. The study referenced in Clinical Background was performed using the TeraGrid.

Click on any of the images in this tutorial to display a larger version of the image.

Login

LDDMM BIRN Portal

LDDMM processing using the sample hippocampus data will take approximately three hours.

Select Dimension

Select Browse

Select Atlas

/home/Public/MorphSASHA__p0002/001446632245/Initial__92_001/shape_analysis__001/lddmm__0001/
   Analysis/Snapshot__001/human/hippocampus/
   registered_80_96_80/001446632245_lh.hippocampus_96.img

Select target

/home/Public/MorphSASHA__p0002/001452043065/Initial__92_001/shape_analysis__001/lddmm__001/
  Analysis/Snapshot__001/human/hippocampus/
  registered_80_96_80/001452043065_lh.hippocampus_96.img

Select 3D image radio button (as this example set is 3 dimensional).

Select output

Launch Job

LDDMM processing using the sample hippocampus data will take approximately three hours.

View Status

InQ

InQ Directory

Get Data through Scommands

[anthony@jhu-gpop anthony]$ Sinit
[anthony@jhu-gpop anthony]$ Scd /home/akolasny.jhu-cis/renewal/XRG_lh.hippocampus_96
[anthony@jhu-gpop anthony]$ Sls
/home/akolasny.jhu-cis/renewal/XRG_lh.hippocampus_96:
  C-/home/akolasny.jhu-cis/renewal/XRG_lh.hippocampus_96/analyze
  C-/home/akolasny.jhu-cis/renewal/XRG_lh.hippocampus_96/txt
  C-/home/akolasny.jhu-cis/renewal/XRG_lh.hippocampus_96/vtk
[anthony@jhu-gpop anthony]$ Scat txt/finalMetricDistance.txt
4.3686689
[anthony@jhu-gpop anthony]$ Scd vtk
[anthony@jhu-gpop anthony]$ Sls
/home/akolasny.jhu-cis/renewal/XRG_lh.hippocampus_96/vtk:
  C-/home/akolasny.jhu-cis/renewal/XRG_lh.hippocampus_96/vtk/deformation_maps
  C-/home/akolasny.jhu-cis/renewal/XRG_lh.hippocampus_96/vtk/deformed_target
  C-/home/akolasny.jhu-cis/renewal/XRG_lh.hippocampus_96/vtk/deformed_template
  C-/home/akolasny.jhu-cis/renewal/XRG_lh.hippocampus_96/vtk/inverse_deformation_maps
  C-/home/akolasny.jhu-cis/renewal/XRG_lh.hippocampus_96/vtk/other
  C-/home/akolasny.jhu-cis/renewal/XRG_lh.hippocampus_96/vtk/velocity_fields
[anthony@jhu-gpop anthony]$ Scd /home/akolasny.jhu-cis/renewal
[anthony@jhu-gpop anthony]$ Sget -b XRG_lh.hippocampus_96 .

Visualize using MayaVi

Using MayaVi

To import the first data set select the File menu (Alt + F). The file menu bar is then displayed.

Select Open (O) on the file menu. A second menu listing file open options is displayed.

Select Vtk File (V) on the this menu. A file selection dialog is displayed.

Navigate to the appropriate directory (deformed_target) and select the desired *.vtk file (MoviedefPatient19.vtk). The data visualizer screen is displayed.

Select Visualize (Alt + V). The visualize menu is displayed.

Select Modules (M). The modules menu is displayed.

Select Isosurface (I). The image is displayed in the Visualization portion of the MayaVi window.

Perform the following actions on the Configure IsoSurface module dialog:

1) check the Compute PolyDataNormals checkbox.

2) Set Opacity to 0.55 using the Set Opacity scroll bar.

3) Close the Configure IsoSurface module dialog.

The first data set is now imported.

Import the second data set using the same procedure as the first data set:

1) File (Alt + F)

2) Open (O)

3) Vtk File (V)

4) Navigate to the appropriate directory (deformed_template) and select the desired *.vtk file (MoviedefAtlas0.vtk)

The first image is still displayed.

Navigate to the Configure IsoSurface module dialog as before:

1) Visualize (Alt + V)

2) Modules (M)

3) Isosurface (I)

Perform the following actions on the Configure IsoSurface module dialog:

1) check the Compute PolyDataNormals checkbox.

2) Deselect the Scalar Coloring checkbox.

3) Select Change Object Color. The Change Object Color dialog is displayed. The Change Object Color dialog differs from Windows to Unix. The Windows dialog is discussed first, followed by unix dialog.

1) Select the desired color using mouse.

1) The desired color parameters are displayed in the edit boxes on the right hand side of the dialog. The color selection also can be input using these edit boxes. Select OK to close the Change objects color dialog.

1) Unix users can enter the desired color as follows. Place cursor in Selection box, and delete value #ffffff. Enter value #007ec0 (hit Return Key after entering this value, before selecting OK button). Select the OK button to apply the color change.

1) The two images can now be clearly distinguished. Set Opacity to 0.55 using the scroll bar and close the Configure IsoSurface Module dialog.

The second data set is now imported.

Import the third data set using the same procedure as the first data set:

1) File (Alt + F)

2) Open (O)

3) Vtk File (V)

4) Navigate to the appropriate directory (velocity_fields) and select the desired *.vtk file (MovieVelocity19.vtk)

Select Visualize (V). The visualize menu bar is displayed.

Select Filters (F). The filter menu is displayed. Select ExtractVectorNorm (V).

The Configure Vector dialog is displayed. Select OK to close the Configure Vector dialog.

Select Filters (F). The filter menu is displayed. Select Threshold (H).

The Configure Threshold dialog is displayed. Enter 2.0 in Minimum threshold edit box. Hit [Return] before selecting Close button. Select Close button on Configure Threshold dialog.

The first two data sets are displayed.

Select Visualize (V) Modules (M) VelocityVector (Y).

The two hippocampus data sets and velocity vectors are now displayed.

Visualize using ParaView

Using ParaView

To import the first data set select the File menu (Alt + F). The file menu bar is then displayed.

Select Open Data (O) on the file menu. A file selection dialog is displayed.

Navigate to the appropriate directory (deformed_target) and select the desired *.vtk file (MoviedefPatient9.vtk). The data visualizer screen is displayed.

Move cursor to the "Generate Isolines or Isosurfaces" icon. This is the ninth icon from the left on the toolbar.

Select the icon using the left mouse button. The modules menu is displayed.

Select the "Accept" button. The Isosurface is displayed in the 3D View window.

Select the Display tab.

Locate the "Actor Color" dialog (in the Color group).

Select a color and press the "OK Button".

Set "Opacity" to 0.5 in the lowermost control.

Import the second data set using the same procedure as the first data set:

1) File (Alt + F)

2) Open Data (O)

3) Navigate to the appropriate directory (deformed_template) and select the desired *.vtk file (MoviedefAtlas0.vtk)

The first image is still displayed.

As before, select the "Display" tab, change the color of the second isosurface, and set opacity to 0.5.

Import the third data set using the same procedure as the first data set:

1) File (Alt + F)

2) Open Data (O)

3) Navigate to the appropriate directory (velocity_fields) and select the desired *.vtk file (MovieVelocity9.vtk). For large data set, this may take some time (tens of seconds).

Select "Generate a Glyph" icon. This is the tenth icon from the left on the toolbar.

Select the "Accept" button. The template and target isosurfaces are displayed, as well as velocity vectors.

Acknowledgements:

ParaView image data courtesy Alexandra Badea, Ph.D. Duke Center for In Vivo Microscopy

Mouse BIRN

Last Modified: Friday, 17-Aug-2007 13:24:48 EDT