[ITK] Determine surface area of certain region in image

Wed Aug 10 09:27:05 EDT 2016

Sorry, I have confused LabelShapeStatistics
<https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1LabelShapeStatisticsImageFilter.html>
with LabelStatistics
<https://itk.org/Doxygen/html/classitk_1_1LabelStatisticsImageFilter.html>
filter.

With label shape statistics, there is no intensity image, only the label
image which you are already using as input.

You generally don't mix (add) label and intensity images, you just keep
them separate and know which two are a pair. For label statistics, you
simply set two inputs like in this example
<https://itk.org/Wiki/ITK/Examples/ImageProcessing/LabelStatisticsImageFilter>
.

Regards

On Wed, Aug 10, 2016 at 9:19 AM, Matthias B <matthias.b at hotmail.com> wrote:

> I understand, but how do I add the label on the 3D image programmatically?
> preferable in C#, but C++ is also ok.
>
> Thank you for your help
> ------------------------------
> From: dzenanz at gmail.com
> Date: Wed, 10 Aug 2016 09:14:35 -0400
> Subject: Re: [ITK] Determine surface area of certain region in image
> To: matthias.b at hotmail.com
> CC: blowekamp at mail.nih.gov; dan.muel at gmail.com; community at itk.org
>
>
> The 3D image where the label will be applied is need for statistics such
> as mean, min and max values. If you don't care about those, you can supply
> the same image as both label and original (intensity) image. Or you can
> supply an empty (all black) image there.
>
> HTH,
> Dženan
>
> On Wed, Aug 10, 2016 at 8:47 AM, Matthias B <matthias.b at hotmail.com>
> wrote:
>
> Thank you for answering Dženan,
>
> ok, the perimeter attribute is what I need.
>
> Problem is that I don't see a way where I can
> 1. Choose a label image to define the region
> 2. Choose the 3D Image where the label will be aplied
>
> At this moment it looks for me that the label image already contains the
> 3D data, which confuses me.
>
> ------------------------------
> From: dzenanz at gmail.com
> Date: Wed, 10 Aug 2016 08:32:53 -0400
> Subject: Re: [ITK] Determine surface area of certain region in image
> To: matthias.b at hotmail.com
> CC: blowekamp at mail.nih.gov; community at itk.org
>
>
> Hi Matthias,
>
> perimeter should be surface area in 3D (which you can divide by 2 to
> eliminate back side if you have a very flat object). In 2D image, it is the
> circumference. In 2D image, you can get object's surface area by counting
> how many pixels it has and then multiplying that by the size of each pixel
> (spacing[0]*spacing[1]).
>
> Regards,
> Dženan
>
> On Wed, Aug 10, 2016 at 2:40 AM, Matthias B <matthias.b at hotmail.com>
> wrote:
>
> Thank you for answering!
>
> At this moment I get the perimeter in pixel units (not the surface area of
> my X,Y-data) of my labeled image.
> I have also really no idea how to use my 3D data with a labeled image. I
> see no way how to add 3D data to a LabelMap for example.
>
> This is what I have at the moment.
> Dim labelShapeStatistics = New simple.LabelShapeStatisticsImageFilter()
> labelShapeStatistics.Execute(labelImage)
> Dim perimeterValue= labelShapeStatistics.GetPerimeter(1)
>
> Thanks for any help, Matthias
>
>
>
> ------------------------------
> From: blowekamp at mail.nih.gov
> To: matthias.b at hotmail.com
> CC: community at itk.org
> Subject: Re: [ITK] Determine surface area of certain region in image
> Date: Tue, 9 Aug 2016 15:58:56 +0000
>
>
> Hello,
>
> You should look into the label map framework [1]. In particular the
> LabelImageToShapeLabelMapFilter[2] and the Perimeter attribute [3] [4].
>
> HTH,
> Brad
>
> [1] http://hdl.handle.net/1926/584
> [2] https://itk.org/Doxygen/html/classitk_1_1LabelImageToSha
> peLabelMapFilter.html
> [3] https://itk.org/Doxygen/html/classitk_1_1ShapeLabelObjec
> t.html#aff1209e925293c15775520ef89e97afb
> [4] http://hdl.handle.net/10380/3342
>
> On Aug 9, 2016, at 11:50 AM, Matthias B <matthias.b at hotmail.com> wrote:
>
> Hello ITK-community,
>
> At the moment I'm working with 3D Images with following structure:
> 100x80x3. Every pixel contains a X,Y,Z value.
> I want to calculate the surface area of a certain region that I have
> defined with a boolean 2D-Image (100x80).
> The surface area should only be calculated with the X,Y-data.
>
> In Matlab I have experience with this by using the function bwboundaries
> on the boolean image. This function determines the indices of the the
> boundaries in clockwise direction.  Next I take the corresponding X,Y
> values of the indices so I can calculate the surface area with the function
> polyarea.
>
> Is this possbile with the ITK-library?
>
> Thank you for your help guys.
>
>
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