[Insight-users] Regarding Fast Marching

[Dawood Al Masslawi]

The best way for selecting a threshold is using the user provided feedback
by interactive means.

The best you can do is to select the closest threshold to the tumor
boundary, usually after

a little trial-and-error the best threshold is identified.

As Kevin pointed out use the intensity difference between tissues as a cue
for the threshold.

At first start with a large threshold then decrease it till you get the
right amount of details in

the segmented image.

Best regards,

Dawood


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On Mon, Jun 20, 2011 at 8:26 AM, amit satish <amitsatish.unde at teamta.in>wrote:

> **
> On 6/18/2011 5:40 PM, Dawood Al Masslawi wrote:
>
> Hi Amit,
>
>  In addition to what Kevin said, select the Alpha and Beta values such
> that the regions you want to
>
>  segment would be emphasized in the resulting image, for an instance, make
> the bright regions brighter
>
>  if you want to segment the bright regions.
>
>  Choose the value for Sigma based on how much detail you want to include
> in the segmented image,
>
>  lower values will result in more details and higher values will smooth
> more details hence resulting in less
>
>  details in the segmented image.
>
>  Assigning the seed points and the threshold by users (radiologists in
> your case) can be done using Graphical User Interface
>
>  tools such as FLTK or Qt and VTK, but it's probably better to get your
> application up and running before developing a GUI.
>
>  Hope that helps,
>
>  Dawood
>
>
>
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>
>
>  On 06/17/2011 01:39 AM, amitsatish.unde at teamta.in <http://www.itk.org/mailman/listinfo/insight-users> 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.
>
>
>  Dear Sir,
>                Thank you for reply. How to choose proper threshold? Because
> in my case tumor boundary is not clearly visible.
>
>
>
>
> Regards,
> Amit.
>
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