[Insight-users] FastMarchingImageFilter

[Luis Ibanez]

Hi Amitesh,


1) The seed value is the time that you want to assign to
    a particular seed point in order to initialize the
    time crossing map at that point. Just set it to zero.
    You are free to add as many seed points as you want.
    Just set the values of all of them to zero.


    In order to understand the time-crossing map concept
    you may want to read the description of this filter in
    the ITK Software Guide:

       http://www.itk.org/ItkSoftwareGuide.pdf

    and look at the book of Sethian.

       "Level Set Methods and Fast Marching Methods"
http://www.amazon.com/exec/obidos/tg/detail/-/0521645573/qid=1105195504/sr=8-1/ref=sr_8_xs_ap_i1_xgl14/102-7770007-4124926?v=glance&s=books&n=507846





2) This is a common mistake when you use PNG images
    of 16 bits, but the data in the image is in the
    range of 8 bits.  Viewers are expecting values
    in the range 0-65535, but they find values in the
    range 0-255, that are therefore displayed as very
    dark values, making the image look black.

    Solution A: if the dynamic range of your data is 8bits
                then don't store it in 16bit images.

    Solution B: Use as viewer the "ImageViewer" application
                distributed as part of InsightApplications


    Solutino C: Some viewer will allow you to "normalize"
                the image (e.g. display in ImageMagick).




3) BTW notice that VolView has two plugins available for
    computing FastMarching. You simply add seed points as
    "3D Markers".  The binary DLLs are distributed with
    VolView, and the source code of the plugins is
    distributed with InsightApplications.







Regards,


    Luis




-------------------------
Amitesh Agarwal wrote:

> Hi all,
> 
> I am trying to use Fast Marching image Filter for segmentation of a 3D
> greyscale image.
> Below is the header of the .vtk image file.
> 
> # vtk DataFile Version 3.0
> VTK File Generated by Insight Segmentation and Registration Toolkit (ITK)
> BINARY
> DATASET STRUCTURED_POINTS
> DIMENSIONS 256 256 100
> SPACING 0.9375 0.9375 2
> ORIGIN 0 0 0
> POINT_DATA 6553600
> SCALARS scalars unsigned_short 1
> LOOKUP_TABLE default
> 
> 1) I wanted to use multiple seed point for the segmentation but I am
> not sure what does the seedValue means and how can I find out for for
> my image what value I should put in.
> Moreover for multiple seed points how will the seed value of one
> seedpoint in the image will differ from seedvalue of another seedpoint
> in the image data?
> 
> typedef FastMarchingFilterType::NodeType                NodeType; 
> NodeType node;
> const double seedValue = 0.0; //what does seedvalue means?
> node.SetValue( seedValue );  
> 
> 2) When I make slices of the image data in .png format, I find using
> any viewer that the image generated is blank (or the viewer is not
> able to interprate the data) . But I know that image is there and
> infact the data is not blank as I can visualize the 3D .vtk data with
> VolView from which I have made .png slices.
> 
> How can I solve the Problem?
> 
> Thanks 
> 
> Amitesh
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>