# Extract bone

**URL:** https://discourse.itk.org/t/extract-bone/2869
**Category:** Beginner Questions
**Tags:** simpleitk
**Created:** [March 23, 2020, 7:41am UTC](https://discourse.itk.org/t/extract-bone/2869 "2020-03-23T07:41:26Z")
**Posts on this page:** 9
**Page:** 1

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### Author: ![flaviu2](https://discourse.itk.org/letter_avatar_proxy/v4/letter/f/74df32/32.png) [@flaviu2](https://discourse.itk.org/u/flaviu2)
#### Post date: [March 23, 2020, 7:41am UTC](https://discourse.itk.org/t/extract-bone/2869/1 "2020-03-23T07:41:26Z")

</div>

I have few pieces of ideas/code, but I cannot connect them to achieve _extraction / removing_ of a bone from a volume ( **vtkVolume** ), with **SimpleITK**.

I know that I need to make a segmentation on the initial image. And I have tried [sitk::SLIC](https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1SLICImageFilter.html)

After that, I have labeled the outcome with **LabelIntensityStatisticsImageFilter**.

```
Label: {1} -> Mean: {368.290207} Size: {566.464000}
Label: {2} -> Mean: {2526.748027} Size: {1077.480000}
Label: {3} -> Mean: {1322.812512} Size: {2101.808000}
Label: {4} -> Mean: {5.314739} Size: {1655.520000}
Label: {5} -> Mean: {1152.650079} Size: {2021.784000}
Label: {7} -> Mean: {1261.300340} Size: {1532.264000}
Label: {8} -> Mean: {0.115451} Size: {1778.208000}
.....
....
Label: {65} -> Mean: {1173.982044} Size: {2118.912000}
Label: {66} -> Mean: {1282.010115} Size: {1144.464000}
Label: {67} -> Mean: {2.750152} Size: {1684.992000}
Label: {68} -> Mean: {1828.256807} Size: {1617.560000}
Label: {69} -> Mean: {744.446380} Size: {1679.000000}
Label: {70} -> Mean: {2429.636374} Size: {1005.144000}
Label: {71} -> Mean: {0.000000} Size: {1710.064000}
Label: {72} -> Mean: {1037.654082} Size: {1918.584000}
...
...
Label: {205} -> Mean: {661.414440} Size: {2436.288000}
Label: {206} -> Mean: {742.483240} Size: {1631.552000}
Label: {207} -> Mean: {923.733392} Size: {537.688000}
Label: {208} -> Mean: {1080.068644} Size: {410.816000}
Label: {209} -> Mean: {643.469645} Size: {258.800000}

```

Now, how can I take from those labels the bones only (_is CBCT_), and use it to remove it from the final **sitk::Image**? What are the next filter that should I use these labels to remove bones from the volume ?

Thank you for your time and patience.

Flaviu.

P.S. If I use **sitk::ConnectedComponent** instead of [sitk::SLIC](https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1SLICImageFilter.html) I got only two labels (from a complete CBCT):

```
Label: {1} -> Mean: {1049.634946} Size: {179605.928000}
Label: {2} -> Mean: {12.000000} Size: {0.016000}
```

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<div class="post-metadata">

### Author: ![flaviu2](https://discourse.itk.org/letter_avatar_proxy/v4/letter/f/74df32/32.png) [@flaviu2](https://discourse.itk.org/u/flaviu2)
#### Post date: [March 23, 2020, 3:50pm UTC](https://discourse.itk.org/t/extract-bone/2869/2 "2020-03-23T15:50:47Z")

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> [@flaviu2](#):
>
> LabelIntensityStatisticsImageFilter

From my researches I understand that **sitk::ChangeLabelImageFilter** should be used after **sitk::LabelIntensityStatisticsImageFilter**. But I didn’t found any example: [Search - v5.4.0](https://itk.org/ITKExamples/search.html?q=LabelIntensityStatisticsImageFilter)

Can you tell me how to use this filter ? Or at least if I am the right way …

P.S. I have tried the following code:

```
	sitk::Image imgTemp(imgOrg);
	sitk::Image cc = sitk::ConnectedComponent(imgTemp);
	sitk::LabelIntensityStatisticsImageFilter statistics;
	statistics.Execute(cc, imgTemp);
	std::vector<int64_t>::iterator it;
	std::vector<int64_t> labels = statistics.GetLabels();
	for (it = labels.begin(); it != labels.end(); ++it)
	{
		TRACE(_T("Label: {%lu} -> Mean: {%f} Size: {%f}\n"),
			*it, statistics.GetMean(*it), statistics.GetPhysicalSize(*it));
	}

	std::map<double, double> mapChange;
	mapChange.insert(std::make_pair(1049.634946, 0));

	imgOrg = sitk::ChangeLabel(cc, mapChange);

```

But I have nothing than a diffuse cube … what I have done wrong ? I feel I am not far from the result, I need a little help …

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<div class="post-metadata">

### Author: ![flaviu2](https://discourse.itk.org/letter_avatar_proxy/v4/letter/f/74df32/32.png) [@flaviu2](https://discourse.itk.org/u/flaviu2)
#### Post date: [March 25, 2020, 1:04pm UTC](https://discourse.itk.org/t/extract-bone/2869/3 "2020-03-25T13:04:41Z")

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I come back with a little progress, and with an error:

```
sitk::Image imgTemp(imgOrg);
sitk::Image labels = sitk::SLIC(imgTemp);
sitk::LabelShapeStatisticsImageFilter statistics;
statistics.Execute(labels);

std::vector<int64_t>::iterator it;
std::vector<int64_t> ls = statistics.GetLabels();
std::map<double, double> mapChange;
for (it = ls.begin(); it != ls.end(); ++it)
{
	mapChange.insert(std::make_pair(*it, statistics.GetRoundness(*it) < 0.2 ? 0 : 255));
}

sitk::Image change = sitk::ChangeLabel(labels, mapChange);
imgOrg = sitk::LabelMapToBinary(change); // <-- sitk::ERROR: Pixel type: 32-bit unsigned integer is not supported in 3D byclass itk::simple::LabelMapToBinaryImageFilter

```

but on the last line, _imgOrg = sitk::LabelMapToBinary(change);_, I got the following error:

`sitk::ERROR: Pixel type: 32-bit unsigned integer is not supported in 3D byclass itk::simple::LabelMapToBinaryImageFilter`

What is the way to overcome this error ?

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### Author: ![blowekamp](https://discourse.itk.org/user_avatar/discourse.itk.org/blowekamp/32/79_2.png) [@blowekamp](https://discourse.itk.org/u/blowekamp)
#### Post date: [March 25, 2020, 1:58pm UTC](https://discourse.itk.org/t/extract-bone/2869/4 "2020-03-25T13:58:56Z")

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The `LabelMapToBinaryImageFilter` operates of Images which have a `sitkLabel` pixels type, not regular integers. You can use `NotEqual(change, 0)` to do a similar operation on scalar images.

---

<div class="post-metadata">

### Author: ![flaviu2](https://discourse.itk.org/letter_avatar_proxy/v4/letter/f/74df32/32.png) [@flaviu2](https://discourse.itk.org/u/flaviu2)
#### Post date: [March 25, 2020, 2:32pm UTC](https://discourse.itk.org/t/extract-bone/2869/5 "2020-03-25T14:32:59Z")

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Kindly thank you Bradley, I get rid of that error. But I have to continue to dig in, because after all code from above, even corrected, I got only a diffuse cube, with only small part of opaque brown piece. By now, I only shoot in the dark 😀 …

---

<div class="post-metadata">

### Author: ![flaviu2](https://discourse.itk.org/letter_avatar_proxy/v4/letter/f/74df32/32.png) [@flaviu2](https://discourse.itk.org/u/flaviu2)
#### Post date: [March 25, 2020, 3:32pm UTC](https://discourse.itk.org/t/extract-bone/2869/6 "2020-03-25T15:32:03Z")

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I have tried sitk:: **LabelIntensityStatisticsImageFilter** instead of sitk:: **LabelShapeStatisticsImageFilter** , with pretty same result. And I guess I got the same result because I still don’t get it what should I put in **changeMap** from **sitk::ChangeLabel** As _key_, and as _value_.

```
	sitk::Image imgTemp(imgOrg);
	sitk::Image cc = sitk::SLIC(imgTemp);
	sitk::LabelIntensityStatisticsImageFilter statistics;
	statistics.Execute(cc, imgTemp);

	std::vector<int64_t> ls = statistics.GetLabels();
	std::map<double, double> mapChange;
	for (it = ls.begin(); it != ls.end(); ++it)
	{
		os << *it << "\t" << statistics.GetMean(*it) << "\t" << statistics.GetPhysicalSize(*it)
			<< "\t" << statistics.GetRoundness(*it) << std::endl;
		mapChange.insert(std::make_pair(*it, statistics.GetPhysicalSize(*it) < 500 ? statistics.GetPhysicalSize(*it) : 0));
	}

```

As **map** key, is ok \ ***it**?

And as **value** , \*statistics.GetRoundness(_it)_, or \*statistics.GetPhysicalSize(_it)_ or \*statistics.GetMean(_it)_ ? Or what ? I haven’t found any documentation regarding this …

I think once I’ll understand this, my chance to solve my task will increase … I’ll be very grateful for any clarification here.

Thank you for your time.

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<div class="post-metadata">

### Author: ![flaviu2](https://discourse.itk.org/letter_avatar_proxy/v4/letter/f/74df32/32.png) [@flaviu2](https://discourse.itk.org/u/flaviu2)
#### Post date: [March 25, 2020, 7:40pm UTC](https://discourse.itk.org/t/extract-bone/2869/7 "2020-03-25T19:40:51Z")

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I guess I figure out what should put in that mapChange:

```
		if(statistics.GetRoundness(*it) < 0.2)
			mapChange.insert(std::make_pair(*it, 0));

```

and the following filter are:

```
	sitk::Image change = sitk::ChangeLabel(cc, mapChange);
	imgOuput = sitk::NotEqual(change, 0);

```

The problem is that the imgOutput look like that (CBCT):

![image](https://discourse.itk.org/uploads/default/original/2X/e/e8fc23ad32c4dcba67131ae32ea0cd04dc586943.png)

Strange … the filters from output are not the right one … I continue to shoot … in the dark … 😀

---

<div class="post-metadata">

### Author: ![dzenanz](https://discourse.itk.org/user_avatar/discourse.itk.org/dzenanz/32/1093_2.png) [@dzenanz](https://discourse.itk.org/u/dzenanz)
#### Post date: [March 25, 2020, 8:03pm UTC](https://discourse.itk.org/t/extract-bone/2869/8 "2020-03-25T20:03:38Z")

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Instead of “shooting in the dark”, you could go through [Segmentation chapter](https://itk.org/ITKSoftwareGuide/html/Book2/ITKSoftwareGuide-Book2ch4.html) of ITK software guide to get a better start.

---

<div class="post-metadata">

### Author: ![flaviu2](https://discourse.itk.org/letter_avatar_proxy/v4/letter/f/74df32/32.png) [@flaviu2](https://discourse.itk.org/u/flaviu2)
#### Post date: [March 25, 2020, 8:37pm UTC](https://discourse.itk.org/t/extract-bone/2869/9 "2020-03-25T20:37:32Z")

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Ok, I’ll read it all, even I have read another documentation about this … seem that I haven’t paid enough attention as long I cannot solve my issue.