Beginner question about how to pick out certain bones of X ray DICOM file with "Threshold Frequency" settings to make desired STL files

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Beginner question about how to pick out certain bones of X ray DICOM file with "Threshold Frequency" settings to make desired STL files

Christian Seberino

I wanted to humbly ask a question about creating STL files from DICOM files
with 3D Slicer.

I got it to work and needed some help about a specific step that's confusing.....

There is a step where you specify the "threshold frequency" after you click the “Threshold Effect” button.
That causes more or less of the bones in a DICOM image to be present in the final STL file.
I'm confused how people find the right setting for the threshold  frequency.  For example, suppose you
had a picture of a skull or jaw and just wanted to the TEETH to end up in an STL file.

How in the world do you find the perfect "threshold frequency" to just see the teeth if that is what you want?

Thanks in advance.

Sincerely,

Dr. Chris S.



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Re: Beginner question about how to pick out certain bones of X ray DICOM file with "Threshold Frequency" settings to make desired STL files

Murat Maga

This will depend on the imaging modality and how much difference there is between tissue types. Based on your example, I will assume your modality is CT or microCT, in which the grayscale values are related to the X-ray attenuation of the tissue. Dentition is the most heavily mineralized tissue, so they will be located at the upper end of the grayscale values. So when you are in the editor and threshold effect, use the slider to define the threshold range you want to retain (everything else is gets set to zero), until you pick just the teeth nothing else. This will only work for the crown part of the tooth, since roots have grayscale values that overlap with those of the mandible or the skull. If you want to retain the roots, a simple threshold will not work for you, but you need to interactively segment the root.

 

You can read more about the Editor and step and step segmentation at:

http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial.html

 

It refers to an older version of slicer but everything should still hold for the current version.

M

 

 

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Christian Seberino
Sent: Saturday, May 21, 2016 7:32 PM
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Beginner question about how to pick out certain bones of X ray DICOM file with "Threshold Frequency" settings to make desired STL files

 

 

I wanted to humbly ask a question about creating STL files from DICOM files

with 3D Slicer.

 

I got it to work and needed some help about a specific step that's confusing.....

 

There is a step where you specify the "threshold frequency" after you click the “Threshold Effect” button.

That causes more or less of the bones in a DICOM image to be present in the final STL file.

I'm confused how people find the right setting for the threshold  frequency.  For example, suppose you

had a picture of a skull or jaw and just wanted to the TEETH to end up in an STL file.

 

How in the world do you find the perfect "threshold frequency" to just see the teeth if that is what you want?

 

Thanks in advance.

 

Sincerely,

 

Dr. Chris S.

 

 


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Re: Beginner question about how to pick out certain bones of X ray DICOM file with "Threshold Frequency" settings to make desired STL files

Christian Seberino
In reply to this post by Christian Seberino
Murat, et al

Thanks!  I assume every DICOM image for every person is different?  I suppose it is just wishful thinking to hope the same settings will work with all teeth of different people?  Or perhaps everyone's teeth show up with pretty much the same grayscale values?  That would be VERY nice if that were true!?

cs
the same greyscale values?


On Sat, May 21, 2016 at 11:32 PM, Murat Maga <[hidden email]> wrote:

This will depend on the imaging modality and how much difference there is between tissue types. Based on your example, I will assume your modality is CT or microCT, in which the grayscale values are related to the X-ray attenuation of the tissue. Dentition is the most heavily mineralized tissue, so they will be located at the upper end of the grayscale values. So when you are in the editor and threshold effect, use the slider to define the threshold range you want to retain (everything else is gets set to zero), until you pick just the teeth nothing else. This will only work for the crown part of the tooth, since roots have grayscale values that overlap with those of the mandible or the skull. If you want to retain the roots, a simple threshold will not work for you, but you need to interactively segment the root.

 

You can read more about the Editor and step and step segmentation at:

http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial.html

 

It refers to an older version of slicer but everything should still hold for the current version.

M

 

 

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Christian Seberino
Sent: Saturday, May 21, 2016 7:32 PM
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Beginner question about how to pick out certain bones of X ray DICOM file with "Threshold Frequency" settings to make desired STL files

 

 

I wanted to humbly ask a question about creating STL files from DICOM files

with 3D Slicer.

 

I got it to work and needed some help about a specific step that's confusing.....

 

There is a step where you specify the "threshold frequency" after you click the “Threshold Effect” button.

That causes more or less of the bones in a DICOM image to be present in the final STL file.

I'm confused how people find the right setting for the threshold  frequency.  For example, suppose you

had a picture of a skull or jaw and just wanted to the TEETH to end up in an STL file.

 

How in the world do you find the perfect "threshold frequency" to just see the teeth if that is what you want?

 

Thanks in advance.

 

Sincerely,

 

Dr. Chris S.

 

 




--
_______________________________________

Christian Seberino, Ph.D.
Phone: (936) 828-8747
Email: [hidden email]
_______________________________________



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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: Beginner question about how to pick out certain bones of X ray DICOM file with "Threshold Frequency" settings to make desired STL files

Murat Maga
In reply to this post by Christian Seberino

That will depend on whether your scans are calibrated or not. I am not a medical imaging person, but my understanding is most medical imaging facilities will calibrate the scans, such that bone value always corresponds to the same value (barring the biological variation in the mineral density). So tooth values should be the same as well.

 

In the small animal imaging realm that is most certainly NOT the case. Having said that, most centers will use a fixed scanning and reconstruction protocol as such that grayscale value from one sample to the next sample should change (again barring the biological variations), at least not by much.

 

If all your scans are different, then you may want to do a histogram normalization between them…

 

M

 

 

 

From: Christian Seberino [mailto:[hidden email]]
Sent: Saturday, May 21, 2016 9:48 PM
To: Murat Maga <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: Beginner question about how to pick out certain bones of X ray DICOM file with "Threshold Frequency" settings to make desired STL files

 

Murat, et al

 

Thanks!  I assume every DICOM image for every person is different?  I suppose it is just wishful thinking to hope the same settings will work with all teeth of different people?  Or perhaps everyone's teeth show up with pretty much the same grayscale values?  That would be VERY nice if that were true!?

 

cs

the same greyscale values?

 

 

On Sat, May 21, 2016 at 11:32 PM, Murat Maga <[hidden email]> wrote:

This will depend on the imaging modality and how much difference there is between tissue types. Based on your example, I will assume your modality is CT or microCT, in which the grayscale values are related to the X-ray attenuation of the tissue. Dentition is the most heavily mineralized tissue, so they will be located at the upper end of the grayscale values. So when you are in the editor and threshold effect, use the slider to define the threshold range you want to retain (everything else is gets set to zero), until you pick just the teeth nothing else. This will only work for the crown part of the tooth, since roots have grayscale values that overlap with those of the mandible or the skull. If you want to retain the roots, a simple threshold will not work for you, but you need to interactively segment the root.

 

You can read more about the Editor and step and step segmentation at:

http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial.html

 

It refers to an older version of slicer but everything should still hold for the current version.

M

 

 

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Christian Seberino
Sent: Saturday, May 21, 2016 7:32 PM
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Beginner question about how to pick out certain bones of X ray DICOM file with "Threshold Frequency" settings to make desired STL files

 

 

I wanted to humbly ask a question about creating STL files from DICOM files

with 3D Slicer.

 

I got it to work and needed some help about a specific step that's confusing.....

 

There is a step where you specify the "threshold frequency" after you click the “Threshold Effect” button.

That causes more or less of the bones in a DICOM image to be present in the final STL file.

I'm confused how people find the right setting for the threshold  frequency.  For example, suppose you

had a picture of a skull or jaw and just wanted to the TEETH to end up in an STL file.

 

How in the world do you find the perfect "threshold frequency" to just see the teeth if that is what you want?

 

Thanks in advance.

 

Sincerely,

 

Dr. Chris S.

 

 



 

--

_______________________________________

Christian Seberino, Ph.D.
Phone: (936) 828-8747
Email: [hidden email]
_______________________________________


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
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Re: Beginner question about how to pick out certain bones of X ray DICOM file with "Threshold Frequency" settings to make desired STL files

Murat Maga
In reply to this post by Christian Seberino

Caught a typo. Meant to say that “from one sample to the next sample should NOT change (again barring the biological variations),”

 

Sorry,

M

 

From: Murat Maga
Sent: Saturday, May 21, 2016 10:09 PM
To: 'Christian Seberino' <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: RE: Beginner question about how to pick out certain bones of X ray DICOM file with "Threshold Frequency" settings to make desired STL files

 

That will depend on whether your scans are calibrated or not. I am not a medical imaging person, but my understanding is most medical imaging facilities will calibrate the scans, such that bone value always corresponds to the same value (barring the biological variation in the mineral density). So tooth values should be the same as well.

 

In the small animal imaging realm that is most certainly NOT the case. Having said that, most centers will use a fixed scanning and reconstruction protocol as such that grayscale value from one sample to the next sample should change (again barring the biological variations), at least not by much.

 

If all your scans are different, then you may want to do a histogram normalization between them…

 

M

 

 

 

From: Christian Seberino [[hidden email]]
Sent: Saturday, May 21, 2016 9:48 PM
To: Murat Maga <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: Beginner question about how to pick out certain bones of X ray DICOM file with "Threshold Frequency" settings to make desired STL files

 

Murat, et al

 

Thanks!  I assume every DICOM image for every person is different?  I suppose it is just wishful thinking to hope the same settings will work with all teeth of different people?  Or perhaps everyone's teeth show up with pretty much the same grayscale values?  That would be VERY nice if that were true!?

 

cs

the same greyscale values?

 

 

On Sat, May 21, 2016 at 11:32 PM, Murat Maga <[hidden email]> wrote:

This will depend on the imaging modality and how much difference there is between tissue types. Based on your example, I will assume your modality is CT or microCT, in which the grayscale values are related to the X-ray attenuation of the tissue. Dentition is the most heavily mineralized tissue, so they will be located at the upper end of the grayscale values. So when you are in the editor and threshold effect, use the slider to define the threshold range you want to retain (everything else is gets set to zero), until you pick just the teeth nothing else. This will only work for the crown part of the tooth, since roots have grayscale values that overlap with those of the mandible or the skull. If you want to retain the roots, a simple threshold will not work for you, but you need to interactively segment the root.

 

You can read more about the Editor and step and step segmentation at:

http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial.html

 

It refers to an older version of slicer but everything should still hold for the current version.

M

 

 

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Christian Seberino
Sent: Saturday, May 21, 2016 7:32 PM
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Beginner question about how to pick out certain bones of X ray DICOM file with "Threshold Frequency" settings to make desired STL files

 

 

I wanted to humbly ask a question about creating STL files from DICOM files

with 3D Slicer.

 

I got it to work and needed some help about a specific step that's confusing.....

 

There is a step where you specify the "threshold frequency" after you click the “Threshold Effect” button.

That causes more or less of the bones in a DICOM image to be present in the final STL file.

I'm confused how people find the right setting for the threshold  frequency.  For example, suppose you

had a picture of a skull or jaw and just wanted to the TEETH to end up in an STL file.

 

How in the world do you find the perfect "threshold frequency" to just see the teeth if that is what you want?

 

Thanks in advance.

 

Sincerely,

 

Dr. Chris S.

 

 



 

--

_______________________________________

Christian Seberino, Ph.D.
Phone: (936) 828-8747
Email: [hidden email]
_______________________________________


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
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Re: Beginner question about how to pick out certain bones of X ray DICOM file with "Threshold Frequency" settings to make desired STL files

Kikinis, Ron,M.D.
Hi,

Just to add to what Murat is saying: depending on the source of your data, its calibrated in so-called Hounsfield units. If its a commercial CT, you are in luck, if its a CBCT, most likely not. See the following for some background:

Ron


On May 22, 2016, at 7:27 AM, Murat Maga <[hidden email]> wrote:

Caught a typo. Meant to say that “from one sample to the next sample should NOT change (again barring the biological variations),”
 
Sorry,
M
From: Murat Maga 
Sent: Saturday, May 21, 2016 10:09 PM
To: 'Christian Seberino' <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: RE: Beginner question about how to pick out certain bones of X ray DICOM file with "Threshold Frequency" settings to make desired STL files
 
That will depend on whether your scans are calibrated or not. I am not a medical imaging person, but my understanding is most medical imaging facilities will calibrate the scans, such that bone value always corresponds to the same value (barring the biological variation in the mineral density). So tooth values should be the same as well.
 
In the small animal imaging realm that is most certainly NOT the case. Having said that, most centers will use a fixed scanning and reconstruction protocol as such that grayscale value from one sample to the next sample should change (again barring the biological variations), at least not by much.
 
If all your scans are different, then you may want to do a histogram normalization between them…
 
M
 
 
 
From: Christian Seberino [[hidden email]] 
Sent: Saturday, May 21, 2016 9:48 PM
To: Murat Maga <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: Beginner question about how to pick out certain bones of X ray DICOM file with "Threshold Frequency" settings to make desired STL files
 
Murat, et al
 
Thanks!  I assume every DICOM image for every person is different?  I suppose it is just wishful thinking to hope the same settings will work with all teeth of different people?  Or perhaps everyone's teeth show up with pretty much the same grayscale values?  That would be VERY nice if that were true!?
 
cs
the same greyscale values?
 
 
On Sat, May 21, 2016 at 11:32 PM, Murat Maga <[hidden email]> wrote:
This will depend on the imaging modality and how much difference there is between tissue types. Based on your example, I will assume your modality is CT or microCT, in which the grayscale values are related to the X-ray attenuation of the tissue. Dentition is the most heavily mineralized tissue, so they will be located at the upper end of the grayscale values. So when you are in the editor and threshold effect, use the slider to define the threshold range you want to retain (everything else is gets set to zero), until you pick just the teeth nothing else. This will only work for the crown part of the tooth, since roots have grayscale values that overlap with those of the mandible or the skull. If you want to retain the roots, a simple threshold will not work for you, but you need to interactively segment the root.
 
You can read more about the Editor and step and step segmentation at:
 
It refers to an older version of slicer but everything should still hold for the current version.
M
 
 
From: slicer-users [mailto:[hidden email]] On Behalf Of Christian Seberino
Sent: Saturday, May 21, 2016 7:32 PM
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Beginner question about how to pick out certain bones of X ray DICOM file with "Threshold Frequency" settings to make desired STL files
 
 
I wanted to humbly ask a question about creating STL files from DICOM files
with 3D Slicer.
 
I got it to work and needed some help about a specific step that's confusing.....
 
There is a step where you specify the "threshold frequency" after you click the “Threshold Effect” button.
That causes more or less of the bones in a DICOM image to be present in the final STL file.
I'm confused how people find the right setting for the threshold  frequency.  For example, suppose you
had a picture of a skull or jaw and just wanted to the TEETH to end up in an STL file.
 
How in the world do you find the perfect "threshold frequency" to just see the teeth if that is what you want?
 
Thanks in advance.
 
Sincerely,
 
Dr. Chris S.
 
 


 
-- 

_______________________________________

Christian Seberino, Ph.D.
Phone: (936) 828-8747
Email: [hidden email] 
_______________________________________

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ

-- 
Ron Kikinis, M.D.,
Robert Greenes Distinguished Director of Biomedical Informatics
Professor of Radiology, Harvard Medical School
Director, Surgical Planning Laboratory
http://www.spl.harvard.edu/~kikinis


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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ