[Insight-users] Running the FastMarchingImageFilter.cxx example on 3D data

[Mr Francesco Grussu]

Abayiz, thank you very much for such practical and useful advice.
My regards,

--Francesco

> Hi Francesco,
>
>
> Fast marching computes the arrival time of a front at the points of a
> discrete lattice. In your case, your input first will be smoothed by
> "CurvatureAnisotropicDiffusionImageFilter", then its output will be given
> to the "GradientMagnitudeRecursiveGaussianImageFilter" to calculate its
> gradient. "Sigma" should be set to this filter (you can take a look at the
> gradient calculation formula).
>
>
> The output of this gradient filter is then given to the sigmoid filter to
> calculate its linear transformation, which requires you to provide alpha
> and beta. I usually set sigma=1.0, alpha=-2.0, beta=2.0 for my own case,
> but you should get suitable value by practice. Then this sigmoid output
> will be the input to your fast marching filter. The output of your fast
> marching filter is then given to a binary thresholder to obtain final
> binary output. You should set stopping and threshold values by yourself,
> usually with not a large number, and stopping value is larger than
> threshold value. 
>
> Abayiz
>
>
>
>
> ________________________________
>  From: Mr Francesco Grussu <francesco.grussu at eecs.qmul.ac.uk>
> To: insight-users at itk.org
> Sent: Friday, June 8, 2012 7:02 PM
> Subject: [Insight-users] Running the FastMarchingImageFilter.cxx example
> on 3D data
>
> Dear all,
> I am trying to run the FastMarchingImageFilter.cxx example from the ITK
> Software Guide 2.4.0 ( http://www.itk.org/ITK/resources/software.html ) in
> order to apply a Fast Marching Level Set Segmentation on my own data.
>
> My data are a stack of 260 512x512 2D slices stored in a .nrrd file coming
> from a DICOM series. I have successfully modified the code of the
> FastMarchingImageFilter.cxx example (which deals with a 2D image) in order
> to handle 3D data...
>
> The grey level of the voxel are stored as floating point data and range
> from about -1000 to just under +2000.
>
> I now the three coordinates of a suitable seed point, but I have no idea
> about the other parameters (sigma, alfa, beta, Time Threshold, Stopping
> Value as well as the parameters for the
> CurvatureAnisotropicDiffusionImageFilter called int the example).
>
> Does anyone have even a rough idea about a suitable way to estimate good
> values of that parameters before running the algorithm?
>
> Thanks a lot in advance,
> my regards,
>
> Francesco
>
>
>
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