Edit Images for Geometrical and Materila Properties Fitting

Select Fitting→Edit→Images...

  • In the Edit Images Table Manager select File to load data.
    • Choose Open Image... to load a single image, a browsing interface will pop-up.

      • The image will appear in the window.
    • Choose Open Stack... to load a folder of images, a browsing interface will pop-up.

      • The stack of images will appear in the window, use the Slice scroll bar to check it, Lower Tables→Mask→Threshold→View channel to select Red, Green or Blue channel..

    • Choose Open Afni... to load an afni file, a browsing window will pop-up, see image below. Such interface allows to create RGB image stack on geometry as well as material properties data.

    • Browse for the afni file in the first slot, and browse in the second one for the folder where the image data will create.
      • Geometrical information will be in the folder xyz respectively in Red, Green and Blue channel. Diffusivity tensor component such as dxx,dxy,dxz will be in the folder Dcol1 respectively in Red, Green and Blue channel. Diffusivity tensor component such as dyx,dyy,dyz will be in the folder Dcol2 respectively in Red, Green and Blue channel. Diffusivity tensor component such as dzx,dzy,dzz will be in the folder Dcol3 respectively in Red, Green and Blue channel. First, second and third diffusivity eigenvalue will be in the folder evas respectively in Red, Green and Blue channel. Components of the first eigenvector in x, y and z direction will be in the folder evec1 respectively in Red, Green and Blue channel. Components of the second eigenvector in x, y and z direction will be in the folder evec2 respectively in Red, Green and Blue channel. Components of the third eigenvector in x, y and z direction will be in the folder evec3 respectively in Red, Green and Blue channel. The fractional anisotropy will be in the folder FracAnisotropy in a single b/w channel. Mean diffusivity values will be in the folder MeanDiffusivity in a single b/w channel. Mask contour will be in the folder Mask.

    • In Stack List a list of all created stack will appear, select one to check its images, use the Slice scroll bar to change slice, Lower Tables→Mask→Threshold→View channel to select Red, Green or Blue channel.

  • Upper Tables→Intensity

    • Data Intensity diagram.
  • Upper Tables→Connected Nodes

    • Connected Nodes interface allows to create initial mesh directly on DTI image data to perform geometrical fitting
    • Select… button gives the chance to create a new 2D elements tube Connected Tube…, or duplicate a previous one .Duplicate Previous Tube…

    • Flag on Closed will create or not a closed tube.

    • Through Specify slices... define in which slice plane the initial mesh nodes will create.

    • Flag on Edit Mesh to change nodes position in every specified slice. Flag on Edit Slice to change nodes position in displayed slice.

    • Each yellow dot, see figure above, will produce a node in the initial mesh, use the Cylinder button to add nodes in the slice plane and use the Specify slices… button to specify their orthogonal position. Is worth to observe that number of nodes in each slice as well as number of specified slices define the accuracy of initial mesh.

    • Click on Pointer button to adjust position and orientation of the tube using inner and outer yellow dots ( green if Edit Slice is flagged), right click to delete node.

    • Click on Cylinder button to add nodes, right click to delete node.

    • Use Slice scroll bar to change slice, dots will appear only in the slices specified in Specify slices....

  • Upper Tables→Tranformation

    • Transformation interface scale and set initial mesh in the 3D space.
  • Upper Tables→Stack Rendering

    • Stack Rendering interface allows to set parameters for the rendering in the main continuity graphic interface.
  • Upper Tables→Calculate

    • In Calculate interface different settings for different output are available. Some examples follow.
      • To output the initial mesh in the Create table flag Connected nodes and in the Results table flag Send to Node Form, then click on Calculate. Initial mesh will load in Continuity.

      • To output the contour data in the Create table flag Voxel and in the Results table flag Send to Data Form, use x and y skip to reduce the number of data points, then click on Calculate. Geometrical Data will load in Continuity.

      • To output the DTI tensor data in the Create table flag Tensor and in the Results table flag Send to Data Form, use x and y skip to reduce the number of data points, then click on Calculate. DTI tensor Data will load in Continuity.

  • Lower Tables→Mask

    • Using the Mask interface is possible to create different contour labeled by colors for connected geometries in the images stack.
      • In the Threshold table select the channel of data desired ( All, Red, Green, Blue), set the image threshold to define the mask, the mask will apply in the displayed image. Set the 'Slice scroll bar on the first slice and click on Apply threshold to subsequent images in stack to use the same mask settings on each slice.

      • Label connected components button defines different contours in the mask. Set the 'Slice scroll bar on the first slice and flagApply to subsequent images in stack to define contours through the whole stack.

      • Label Edges button gives a different color label for each different contours created. Use Label Manager... to check and edit labels.

  • Once contours will create click on Pointer button to edit. A pencil will appear, chose the label color, and edit the respective contour. To delete contour use black color. Right click will fill closed area.