[Insight-users] Regarding Fast Marching

[Kevin H. Hobbs]

On 06/17/2011 01:39 AM, amitsatish.unde at teamta.in wrote:
> I am using ItK fast marching for liver tumor segmentation. I want to select manually seed point and output is segmented tumor. My problems is as below,
> 1.can you specify exact value of alpha,beta and sigma for all examples?
> 2.it's very difficult to give threshold value everytime. I am trying to implement a method such that radiologists will choose seed point in tumor region and our algorithm will give exact boundary of tumor. All other parameters i want to set by me.
>
>
> Regards,
> Amit

The parameters used in the software guide for the fast marching
example are listed at the top of the source code :

//  Software Guide : BeginCommandLineArgs
//    INPUTS: {BrainProtonDensitySlice.png}
//    OUTPUTS: {FastMarchingImageFilterOutput5.png}
//    81 114 1.0  -0.5  3.0   100 100
//  Software Guide : EndCommandLineArgs
//  Software Guide : BeginCommandLineArgs
//    INPUTS: {BrainProtonDensitySlice.png}
//    OUTPUTS: {FastMarchingImageFilterOutput6.png}
//    99 114 1.0  -0.5  3.0   100 100
//  Software Guide : EndCommandLineArgs
//  Software Guide : BeginCommandLineArgs
//    INPUTS: {BrainProtonDensitySlice.png}
//    OUTPUTS: {FastMarchingImageFilterOutput7.png}
//    56 92 1.0  -0.3  2.0   200 100
//  Software Guide : EndCommandLineArgs
//  Software Guide : BeginCommandLineArgs
//    INPUTS: {BrainProtonDensitySlice.png}
//    OUTPUTS: {FastMarchingImageFilterOutput8.png}
//    OUTPUTS: [FastMarchingFilterOutput1.png]
//    OUTPUTS: [FastMarchingFilterOutput2.png]
//    OUTPUTS: [FastMarchingFilterOutput3.png]
//    40 90 0.5  -0.3  2.0   200 100
//  Software Guide : EndCommandLineArgs

Unfortunately, the parameters are there for a reason, one value
does not always work well for all images.

My advice to you is to take the example programs and to cut them
up into the smallest usable pieces so that you can actually look
at the images at each step. For the fast marching example you'd
end up with 5 tiny programs :

reader -> smoother           -> writer
reader -> gradient magnitude -> writer
reader -> sigmoid            -> writer
reader -> fast marching      -> writer
reader -> threshold          -> writer

Take a typical example of your images and open it up in ParaView
(or your viewer of choice).

You'll probably find that the intensity profile through the
object you're interested in is bumpy :
                                                 oo
                              oooooo   oo    oo
        o          oo                  oo           o         o
oooo ooo oo    ooo                             ooooo oooo

adjust the parameters of the smoothing filter until the profile
looks as much like this as possible:

                                ooooooooooooo
                              o                          o
ooooooooooooooo                              ooooooooo


adjust the parameters of the gradient magnitude filter until it
looks like this :
                              o                            o
                            o  o                        o  o
oooooooooooooo      ooooooooooo      oooooooo


sigmoid :

ooooooooooooooo oooooooooooooo oooooooooo

                              o                            o

fast :

                              o                            o
                                 o                       o
                                   o                   o
                                     o               o
                                        o          o
                                           o     o
                                              oo

the point is LOOK at the intermediate images.

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