[Insight-users] ParaView : Tutorial in 20 minutes + 2 Cups of Coffee

[Luis Ibanez]

Hi Bing,

Here is a 20 minutes tutorial on how to use
ParaView for viewing vector deformation fields.

First,
get some coffee,..


Session One :
    Objective:          viewing 3D datasets
    Time to complete:   10 minutes

0) Download ParaView from

            http://www . paraview . org

    It is open-source and
    free as in "freedom" and as in "free beer".


1) Start paraview


2) Go to the menu "File"->"Open"
    and load one of the brainweb images

    You can get these images from:
      ftp://public . kitware . com/pub/itk/Data

     ParaView supports reading from RAW image
     data and as VTK file format. Load the
     file

           brainweb1e5a10f17.raw

      in the left panel select:

         Data type  = unsigned char
         Byte order = little endian
         FileDimensionality = 3
         Origin  0 0 0
         Spacing 1 1 1
         Extent  0 180  0 216 0 179
         Num.components   1

     Then click on the "red" button "Accept".
     This button will turn red every time that
     you modify data associated with the dataset.
     The display will only be updated when you
     click on the "Accept" button.

3)  In the same panel select the "Display" tab
     and click on the "Set View to Data" button.
     This will scale and center the data in the
     display window.

4)  Go to the menu bar and select "Filter",
     then "Cut". This will add a cutting plane
     to the data.
     You will see a plane and an orthogonal arrow
     crossing it. You can change the position of
     the plane by clicking and dragging the arrow
     head, the arrow tail or the sphere at the
     intersection of the arrow and the plane.


5)  On top of the left panel you should now
     have the text:

     brainweb165a10f17.raw  and  Cut0

     click on   brainweb165a10f17.raw

     Then go to the menu bar and select "Filter"
     "contour"   This will generate an isosurface.

     In the lower part of the left panel go to
     "New value" and enter 30, then click on the
     "Add" button and then in "Accept".

     ParaView will extract the isosurface of level
     20 and render it in the display window.


End of session One:

    You graduated in viewing
    single component data with ParaView !





Now,
got the second cup of coffee




Session Two:

   Objective: Viewing displacement vector fields
   Time to complete:  10 minutes

0) In order to generate a vector image you can
    use the example:

    Insight/Examples/Filtering/
              GradientRecursiveGaussianImageFilter.cxx

http://www . itk . org/cgi-bin/cvsweb . cgi/Insight/Examples/Filtering/GradientRecursiveGaussianImageFilter . cxx?cvsroot=Insight

    It will take a scalar image as input and will
    produce a vector image as output. The vector
    image representing the gradient of the input image.

    Once you compile this example you run it as

    GradientRecursiveGaussianImageFilter

    with the arguments

      brainweb165a10f17.mhd   gradient.mhd  1.0

    the output vector image will be saved in the
    files "gradient.mhd" and "gradient.raw"


1) Start ParaView

    Go to the menu bar and select "File"->"Open",
    go for the file "gradient.raw" (not the .mhd)

    on the left panel set:

      Data type :  float
      Byte order:  little endian
      File Dimensionality:  3
      Origin  :  0  0  0
      Spacing :  1  1  1
      Extent  : 0 180  0 216 0 179

     Then click on the "Accept" button

     The outline of the dataset should appear in
     the display window.


2)  Go to the menu bar and select

     "Filter"-->"ExtractVOI"

     This will subsample the vector data set.

     The reason for subsampling is that if you
     visualize a vector placed on every pixel,
     the density of vector on the screen will
     be too high to see anything.

     On the lower part of the left panel select

     Sample rate =  10  10  10

     That will sample one voxel every ten voxels
     along every dimension.

3)  Go to the menu bar and select

     "Filter"->"Glyph"

     On the left panel select

     "Orient"  = vector
     "Scale mode" = scalar
     "Scale factor" = 0.5

     Then click on the Accept button.
     ParaView will render a set of vector
     representing the gradient that you loaded.



That's it !

  You graduated in viewing vector data using ParaView.

  You are now ready for starting to register your 3D
  datasets and using ParaView for visualizing the
  deformation fields.


Now you can attempt to load the vector displacement
field generated from the deformable registration.



  Enjoy ITK and ParaView !



     Luis




-----------------------
Bing Jian wrote:

> Hi everyone,
> 
>   I recalled that Luis mentioned a tool like ParaView can be used to
> visualize the deformation field. I just downloaded the ParaView1.0
> for Windows and tried to use it. It looks very cool but also very
> complicated to use. I even don't know how to view an mhd/raw or
> hdr/img file. I noted there is no MetaImage and Analyse in Supported
> Data Formats. and I don't know what are Extent and Num.component
> in Parameters setting. The on-line help does not give much more
> explanation and seems the User's Guide is still under development.
> 
>   Is there any body who has experience with Paraview and could
> tell me how to visualize the deformation field using it? Many
> thanks in advance!
>