Making 3D .stl model from DICOM files

classic Classic list List threaded Threaded
20 messages Options
Reply | Threaded
Open this post in threaded view
|

Making 3D .stl model from DICOM files

Viraj Belekar
Hello everyone,

Is there a proper tutorial which addresses making 3D models in .stl format from DICOM files? I want to make a 3D model of portal vein system from DICOM files. Also what should be the threshold range for veins?

Thanks and Regards
Viraj Belekar

_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Making 3D .stl model from DICOM files

Csaba Pinter-2

I hope this helps:

https://www.slicer.org/wiki/Documentation/Nightly/Training#Slicer4_3D_Printing

 

Cheers,

csaba

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Viraj Belekar
Sent: Tuesday, March 21, 2017 07:23
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Making 3D .stl model from DICOM files

 

Hello everyone,

 

Is there a proper tutorial which addresses making 3D models in .stl format from DICOM files? I want to make a 3D model of portal vein system from DICOM files. Also what should be the threshold range for veins?

 

Thanks and Regards

Viraj Belekar


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Making 3D .stl model from DICOM files

Viraj Belekar
In reply to this post by Viraj Belekar
Hi Miten,

Can you help me in identifying the threshold range for portal veins? Apparently a lot of extra stuff is attached with the veins in the final 3D model.

Thanks a lot!

Regards
Viraj Belekar

On Tue, Mar 21, 2017 at 5:29 PM, Patel, Miten <[hidden email]> wrote:
Hi Viraj,

Following link and attached tutorial referenced on the web page show the steps to generate an STL from DICOM files.


The tutorial uses the nightly build rather than 4.6 released version. I've tried it with nightly build from around 15 Mar and it worked fine.

The tutorial has extra bits of adding a model etc which you can ignore.

We are due to perform the same task for carotid arteries ie STL generation and also centreline extraction for creating geometry for finite element analysis.

Would appreciate liaising with you on these steps as looks like we are working on similar tasks.

Miten


-------- Original message --------
From: Viraj Belekar <[hidden email]>
Date: 21/03/2017 11:24 (GMT+00:00)
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Making 3D .stl model from DICOM files

Hello everyone,

Is there a proper tutorial which addresses making 3D models in .stl format from DICOM files? I want to make a 3D model of portal vein system from DICOM files. Also what should be the threshold range for veins?

Thanks and Regards
Viraj Belekar


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Making 3D .stl model from DICOM files

Andras Lasso-2

> Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Usually you cannot segment vessels by simple thresholding. It’s normal that opacified vessels have the same intensity as bones or other tissues.

 

You can segment the vessel manually: Find a reasonably good threshold range using the threshold effect and click “Use for masking” instead of “Apply”. Then use the paint tool, select “Sphere brush” option, and follow and paint the vessels.

 

You can also try vessel enhancement filter in VMTK extension to enhance vessels and suppress other structures. The vesselness-filtered image will mostly just contain vasculature, so you can extract the vessel tree in the segment editor automatically, by simple thresholding.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Viraj Belekar
Sent: March 28, 2017 0:32
To: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hi Miten,

 

Can you help me in identifying the threshold range for portal veins? Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Thanks a lot!

 

Regards

Viraj Belekar

 

On Tue, Mar 21, 2017 at 5:29 PM, Patel, Miten <[hidden email]> wrote:

Hi Viraj,

 

Following link and attached tutorial referenced on the web page show the steps to generate an STL from DICOM files.

 

 

The tutorial uses the nightly build rather than 4.6 released version. I've tried it with nightly build from around 15 Mar and it worked fine.

 

The tutorial has extra bits of adding a model etc which you can ignore.

 

We are due to perform the same task for carotid arteries ie STL generation and also centreline extraction for creating geometry for finite element analysis.

 

Would appreciate liaising with you on these steps as looks like we are working on similar tasks.

 

Miten



-------- Original message --------
From: Viraj Belekar <[hidden email]>
Date: 21/03/2017 11:24 (GMT+00:00)
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Making 3D .stl model from DICOM files

Hello everyone,

 

Is there a proper tutorial which addresses making 3D models in .stl format from DICOM files? I want to make a 3D model of portal vein system from DICOM files. Also what should be the threshold range for veins?

 

Thanks and Regards

Viraj Belekar

 


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Making 3D .stl model from DICOM files

Viraj Belekar
In reply to this post by Viraj Belekar
Hello Mr. Andras,

By using the technique described by you. I am able to extract a few blood vessel models. The thing is I need to do blood flow analysis using these models. For that I want the end of these veins to be open so that I can define a different surface on these open ends as inlet or outlet. Can you please help?

PFA: stl file.

Regards
Viraj

On Tue, Mar 28, 2017 at 10:19 AM, Andras Lasso <[hidden email]> wrote:

> Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Usually you cannot segment vessels by simple thresholding. It’s normal that opacified vessels have the same intensity as bones or other tissues.

 

You can segment the vessel manually: Find a reasonably good threshold range using the threshold effect and click “Use for masking” instead of “Apply”. Then use the paint tool, select “Sphere brush” option, and follow and paint the vessels.

 

You can also try vessel enhancement filter in VMTK extension to enhance vessels and suppress other structures. The vesselness-filtered image will mostly just contain vasculature, so you can extract the vessel tree in the segment editor automatically, by simple thresholding.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Viraj Belekar
Sent: March 28, 2017 0:32
To: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hi Miten,

 

Can you help me in identifying the threshold range for portal veins? Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Thanks a lot!

 

Regards

Viraj Belekar

 

On Tue, Mar 21, 2017 at 5:29 PM, Patel, Miten <[hidden email]> wrote:

Hi Viraj,

 

Following link and attached tutorial referenced on the web page show the steps to generate an STL from DICOM files.

 

 

The tutorial uses the nightly build rather than 4.6 released version. I've tried it with nightly build from around 15 Mar and it worked fine.

 

The tutorial has extra bits of adding a model etc which you can ignore.

 

We are due to perform the same task for carotid arteries ie STL generation and also centreline extraction for creating geometry for finite element analysis.

 

Would appreciate liaising with you on these steps as looks like we are working on similar tasks.

 

Miten



-------- Original message --------
From: Viraj Belekar <[hidden email]>
Date: 21/03/2017 11:24 (GMT+00:00)
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Making 3D .stl model from DICOM files

Hello everyone,

 

Is there a proper tutorial which addresses making 3D models in .stl format from DICOM files? I want to make a 3D model of portal vein system from DICOM files. Also what should be the threshold range for veins?

 

Thanks and Regards

Viraj Belekar

 



_______________________________________________
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

vein.stl (759K) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: Making 3D .stl model from DICOM files

Andras Lasso-2
In reply to this post by Viraj Belekar

Would you like to make the model hollow (like a tube)?

 

Andras

 

From: [hidden email]
Sent: Tuesday, March 28, 2017 2:12 AM
To: [hidden email]
Cc: [hidden email]; [hidden email]
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello Mr. Andras,

By using the technique described by you. I am able to extract a few blood vessel models. The thing is I need to do blood flow analysis using these models. For that I want the end of these veins to be open so that I can define a different surface on these open ends as inlet or outlet. Can you please help?

PFA: stl file.

Regards
Viraj

On Tue, Mar 28, 2017 at 10:19 AM, Andras Lasso <[hidden email]> wrote:

> Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Usually you cannot segment vessels by simple thresholding. It’s normal that opacified vessels have the same intensity as bones or other tissues.

 

You can segment the vessel manually: Find a reasonably good threshold range using the threshold effect and click “Use for masking” instead of “Apply”. Then use the paint tool, select “Sphere brush” option, and follow and paint the vessels.

 

You can also try vessel enhancement filter in VMTK extension to enhance vessels and suppress other structures. The vesselness-filtered image will mostly just contain vasculature, so you can extract the vessel tree in the segment editor automatically, by simple thresholding.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Viraj Belekar
Sent: March 28, 2017 0:32
To: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hi Miten,

 

Can you help me in identifying the threshold range for portal veins? Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Thanks a lot!

 

Regards

Viraj Belekar

 

On Tue, Mar 21, 2017 at 5:29 PM, Patel, Miten <[hidden email]> wrote:

Hi Viraj,

 

Following link and attached tutorial referenced on the web page show the steps to generate an STL from DICOM files.

 

 

The tutorial uses the nightly build rather than 4.6 released version. I've tried it with nightly build from around 15 Mar and it worked fine.

 

The tutorial has extra bits of adding a model etc which you can ignore.

 

We are due to perform the same task for carotid arteries ie STL generation and also centreline extraction for creating geometry for finite element analysis.

 

Would appreciate liaising with you on these steps as looks like we are working on similar tasks.

 

Miten



-------- Original message --------
From: Viraj Belekar <[hidden email]>
Date: 21/03/2017 11:24 (GMT+00:00)
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Making 3D .stl model from DICOM files

Hello everyone,

 

Is there a proper tutorial which addresses making 3D models in .stl format from DICOM files? I want to make a 3D model of portal vein system from DICOM files. Also what should be the threshold range for veins?

 

Thanks and Regards

Viraj Belekar

 



_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Making 3D .stl model from DICOM files

Viraj Belekar
In reply to this post by Viraj Belekar
Yes the model should be hollow like a tube as I want to analyse internal flow. If you see the stl file, the ends of the vein are fused which I don't want.


On Tue, 28 Mar 2017 at 5:10 PM, Andras Lasso <[hidden email]> wrote:

Would you like to make the model hollow (like a tube)?

 

Andras

 

From: [hidden email]
Sent: Tuesday, March 28, 2017 2:12 AM
To: [hidden email]
Cc: [hidden email]; [hidden email]


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

Hello Mr. Andras,

By using the technique described by you. I am able to extract a few blood vessel models. The thing is I need to do blood flow analysis using these models. For that I want the end of these veins to be open so that I can define a different surface on these open ends as inlet or outlet. Can you please help?

PFA: stl file.

Regards
Viraj

On Tue, Mar 28, 2017 at 10:19 AM, Andras Lasso <[hidden email]> wrote:

> Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Usually you cannot segment vessels by simple thresholding. It’s normal that opacified vessels have the same intensity as bones or other tissues.

 

You can segment the vessel manually: Find a reasonably good threshold range using the threshold effect and click “Use for masking” instead of “Apply”. Then use the paint tool, select “Sphere brush” option, and follow and paint the vessels.

 

You can also try vessel enhancement filter in VMTK extension to enhance vessels and suppress other structures. The vesselness-filtered image will mostly just contain vasculature, so you can extract the vessel tree in the segment editor automatically, by simple thresholding.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Viraj Belekar
Sent: March 28, 2017 0:32
To: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hi Miten,

 

Can you help me in identifying the threshold range for portal veins? Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Thanks a lot!

 

Regards

Viraj Belekar

 

On Tue, Mar 21, 2017 at 5:29 PM, Patel, Miten <[hidden email]> wrote:

Hi Viraj,

 

Following link and attached tutorial referenced on the web page show the steps to generate an STL from DICOM files.

 

 

The tutorial uses the nightly build rather than 4.6 released version. I've tried it with nightly build from around 15 Mar and it worked fine.

 

The tutorial has extra bits of adding a model etc which you can ignore.

 

We are due to perform the same task for carotid arteries ie STL generation and also centreline extraction for creating geometry for finite element analysis.

 

Would appreciate liaising with you on these steps as looks like we are working on similar tasks.

 

Miten



-------- Original message --------
From: Viraj Belekar <[hidden email]>
Date: 21/03/2017 11:24 (GMT+00:00)
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Making 3D .stl model from DICOM files

Hello everyone,

 

Is there a proper tutorial which addresses making 3D models in .stl format from DICOM files? I want to make a 3D model of portal vein system from DICOM files. Also what should be the threshold range for veins?

 

Thanks and Regards

Viraj Belekar

 



_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Making 3D .stl model from DICOM files

Andras Lasso-2
In reply to this post by Viraj Belekar

To create hollow vessel models, use margin and logical operator effects as described here:

http://slicer-users.65878.n3.nabble.com/Hollow-model-tp4031241p4031242.html

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 28, 2017 7:45
To: Andras Lasso <[hidden email]>
Cc: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Yes the model should be hollow like a tube as I want to analyse internal flow. If you see the stl file, the ends of the vein are fused which I don't want.

 

 

On Tue, 28 Mar 2017 at 5:10 PM, Andras Lasso <[hidden email]> wrote:

Would you like to make the model hollow (like a tube)?

 

Andras

 

From: [hidden email]
Sent: Tuesday, March 28, 2017 2:12 AM
To: [hidden email]
Cc: [hidden email]; [hidden email]


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

Hello Mr. Andras,

 

By using the technique described by you. I am able to extract a few blood vessel models. The thing is I need to do blood flow analysis using these models. For that I want the end of these veins to be open so that I can define a different surface on these open ends as inlet or outlet. Can you please help?

 

PFA: stl file.

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 10:19 AM, Andras Lasso <[hidden email]> wrote:

> Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Usually you cannot segment vessels by simple thresholding. It’s normal that opacified vessels have the same intensity as bones or other tissues.

 

You can segment the vessel manually: Find a reasonably good threshold range using the threshold effect and click “Use for masking” instead of “Apply”. Then use the paint tool, select “Sphere brush” option, and follow and paint the vessels.

 

You can also try vessel enhancement filter in VMTK extension to enhance vessels and suppress other structures. The vesselness-filtered image will mostly just contain vasculature, so you can extract the vessel tree in the segment editor automatically, by simple thresholding.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Viraj Belekar
Sent: March 28, 2017 0:32
To: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hi Miten,

 

Can you help me in identifying the threshold range for portal veins? Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Thanks a lot!

 

Regards

Viraj Belekar

 

On Tue, Mar 21, 2017 at 5:29 PM, Patel, Miten <[hidden email]> wrote:

Hi Viraj,

 

Following link and attached tutorial referenced on the web page show the steps to generate an STL from DICOM files.

 

 

The tutorial uses the nightly build rather than 4.6 released version. I've tried it with nightly build from around 15 Mar and it worked fine.

 

The tutorial has extra bits of adding a model etc which you can ignore.

 

We are due to perform the same task for carotid arteries ie STL generation and also centreline extraction for creating geometry for finite element analysis.

 

Would appreciate liaising with you on these steps as looks like we are working on similar tasks.

 

Miten



-------- Original message --------
From: Viraj Belekar <[hidden email]>
Date: 21/03/2017 11:24 (GMT+00:00)
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Making 3D .stl model from DICOM files

Hello everyone,

 

Is there a proper tutorial which addresses making 3D models in .stl format from DICOM files? I want to make a 3D model of portal vein system from DICOM files. Also what should be the threshold range for veins?

 

Thanks and Regards

Viraj Belekar

 

 


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Making 3D .stl model from DICOM files

Viraj Belekar
In reply to this post by Viraj Belekar
Hello,

How do I install VMTK extension as mentioned in the link provided by you? I am following steps on the mentioned here: https://www.slicer.org/wiki/Slicer4:VMTK#Installation

But I need a password to use this command: git clone https://haehn@.../haehn/VMTK-in-3D-Slicer.git

Thanks

Regards
Viraj

On Tue, Mar 28, 2017 at 5:39 PM, Andras Lasso <[hidden email]> wrote:

To create hollow vessel models, use margin and logical operator effects as described here:

http://slicer-users.65878.n3.nabble.com/Hollow-model-tp4031241p4031242.html

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 28, 2017 7:45
To: Andras Lasso <[hidden email]>
Cc: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Yes the model should be hollow like a tube as I want to analyse internal flow. If you see the stl file, the ends of the vein are fused which I don't want.

 

 

On Tue, 28 Mar 2017 at 5:10 PM, Andras Lasso <[hidden email]> wrote:

Would you like to make the model hollow (like a tube)?

 

Andras

 

From: [hidden email]
Sent: Tuesday, March 28, 2017 2:12 AM
To: [hidden email]
Cc: [hidden email]; [hidden email]


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

Hello Mr. Andras,

 

By using the technique described by you. I am able to extract a few blood vessel models. The thing is I need to do blood flow analysis using these models. For that I want the end of these veins to be open so that I can define a different surface on these open ends as inlet or outlet. Can you please help?

 

PFA: stl file.

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 10:19 AM, Andras Lasso <[hidden email]> wrote:

> Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Usually you cannot segment vessels by simple thresholding. It’s normal that opacified vessels have the same intensity as bones or other tissues.

 

You can segment the vessel manually: Find a reasonably good threshold range using the threshold effect and click “Use for masking” instead of “Apply”. Then use the paint tool, select “Sphere brush” option, and follow and paint the vessels.

 

You can also try vessel enhancement filter in VMTK extension to enhance vessels and suppress other structures. The vesselness-filtered image will mostly just contain vasculature, so you can extract the vessel tree in the segment editor automatically, by simple thresholding.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Viraj Belekar
Sent: March 28, 2017 0:32
To: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hi Miten,

 

Can you help me in identifying the threshold range for portal veins? Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Thanks a lot!

 

Regards

Viraj Belekar

 

On Tue, Mar 21, 2017 at 5:29 PM, Patel, Miten <[hidden email]> wrote:

Hi Viraj,

 

Following link and attached tutorial referenced on the web page show the steps to generate an STL from DICOM files.

 

 

The tutorial uses the nightly build rather than 4.6 released version. I've tried it with nightly build from around 15 Mar and it worked fine.

 

The tutorial has extra bits of adding a model etc which you can ignore.

 

We are due to perform the same task for carotid arteries ie STL generation and also centreline extraction for creating geometry for finite element analysis.

 

Would appreciate liaising with you on these steps as looks like we are working on similar tasks.

 

Miten



-------- Original message --------
From: Viraj Belekar <[hidden email]>
Date: 21/03/2017 11:24 (GMT+00:00)
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Making 3D .stl model from DICOM files

Hello everyone,

 

Is there a proper tutorial which addresses making 3D models in .stl format from DICOM files? I want to make a 3D model of portal vein system from DICOM files. Also what should be the threshold range for veins?

 

Thanks and Regards

Viraj Belekar

 

 



_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Making 3D .stl model from DICOM files

Andras Lasso-2
In reply to this post by Viraj Belekar

VMTK is available now through the extension manager. There is no need to manually download or build anything.

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 29, 2017 3:32
To: Andras Lasso <[hidden email]>
Cc: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello,

 

How do I install VMTK extension as mentioned in the link provided by you? I am following steps on the mentioned here: https://www.slicer.org/wiki/Slicer4:VMTK#Installation

 

But I need a password to use this command: git clone https://haehn@.../haehn/VMTK-in-3D-Slicer.git

 

Thanks

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 5:39 PM, Andras Lasso <[hidden email]> wrote:

To create hollow vessel models, use margin and logical operator effects as described here:

http://slicer-users.65878.n3.nabble.com/Hollow-model-tp4031241p4031242.html

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 28, 2017 7:45
To: Andras Lasso <[hidden email]>
Cc: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Yes the model should be hollow like a tube as I want to analyse internal flow. If you see the stl file, the ends of the vein are fused which I don't want.

 

 

On Tue, 28 Mar 2017 at 5:10 PM, Andras Lasso <[hidden email]> wrote:

Would you like to make the model hollow (like a tube)?

 

Andras

 

From: [hidden email]
Sent: Tuesday, March 28, 2017 2:12 AM
To: [hidden email]
Cc: [hidden email]; [hidden email]


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

Hello Mr. Andras,

 

By using the technique described by you. I am able to extract a few blood vessel models. The thing is I need to do blood flow analysis using these models. For that I want the end of these veins to be open so that I can define a different surface on these open ends as inlet or outlet. Can you please help?

 

PFA: stl file.

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 10:19 AM, Andras Lasso <[hidden email]> wrote:

> Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Usually you cannot segment vessels by simple thresholding. It’s normal that opacified vessels have the same intensity as bones or other tissues.

 

You can segment the vessel manually: Find a reasonably good threshold range using the threshold effect and click “Use for masking” instead of “Apply”. Then use the paint tool, select “Sphere brush” option, and follow and paint the vessels.

 

You can also try vessel enhancement filter in VMTK extension to enhance vessels and suppress other structures. The vesselness-filtered image will mostly just contain vasculature, so you can extract the vessel tree in the segment editor automatically, by simple thresholding.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Viraj Belekar
Sent: March 28, 2017 0:32
To: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hi Miten,

 

Can you help me in identifying the threshold range for portal veins? Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Thanks a lot!

 

Regards

Viraj Belekar

 

On Tue, Mar 21, 2017 at 5:29 PM, Patel, Miten <[hidden email]> wrote:

Hi Viraj,

 

Following link and attached tutorial referenced on the web page show the steps to generate an STL from DICOM files.

 

 

The tutorial uses the nightly build rather than 4.6 released version. I've tried it with nightly build from around 15 Mar and it worked fine.

 

The tutorial has extra bits of adding a model etc which you can ignore.

 

We are due to perform the same task for carotid arteries ie STL generation and also centreline extraction for creating geometry for finite element analysis.

 

Would appreciate liaising with you on these steps as looks like we are working on similar tasks.

 

Miten



-------- Original message --------
From: Viraj Belekar <[hidden email]>
Date: 21/03/2017 11:24 (GMT+00:00)
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Making 3D .stl model from DICOM files

Hello everyone,

 

Is there a proper tutorial which addresses making 3D models in .stl format from DICOM files? I want to make a 3D model of portal vein system from DICOM files. Also what should be the threshold range for veins?

 

Thanks and Regards

Viraj Belekar

 

 

 


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Making 3D .stl model from DICOM files

Viraj Belekar
In reply to this post by Viraj Belekar
Hi Mr. Andras,

I had downloaded the Nightly Build version and VMTK is not available through the extension manager for it.

On Wed, Mar 29, 2017 at 6:24 PM, Andras Lasso <[hidden email]> wrote:

VMTK is available now through the extension manager. There is no need to manually download or build anything.

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 29, 2017 3:32


To: Andras Lasso <[hidden email]>
Cc: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello,

 

How do I install VMTK extension as mentioned in the link provided by you? I am following steps on the mentioned here: https://www.slicer.org/wiki/Slicer4:VMTK#Installation

 

But I need a password to use this command: git clone https://haehn@.../haehn/VMTK-in-3D-Slicer.git

 

Thanks

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 5:39 PM, Andras Lasso <[hidden email]> wrote:

To create hollow vessel models, use margin and logical operator effects as described here:

http://slicer-users.65878.n3.nabble.com/Hollow-model-tp4031241p4031242.html

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 28, 2017 7:45
To: Andras Lasso <[hidden email]>
Cc: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Yes the model should be hollow like a tube as I want to analyse internal flow. If you see the stl file, the ends of the vein are fused which I don't want.

 

 

On Tue, 28 Mar 2017 at 5:10 PM, Andras Lasso <[hidden email]> wrote:

Would you like to make the model hollow (like a tube)?

 

Andras

 

From: [hidden email]
Sent: Tuesday, March 28, 2017 2:12 AM
To: [hidden email]
Cc: [hidden email]; [hidden email]


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

Hello Mr. Andras,

 

By using the technique described by you. I am able to extract a few blood vessel models. The thing is I need to do blood flow analysis using these models. For that I want the end of these veins to be open so that I can define a different surface on these open ends as inlet or outlet. Can you please help?

 

PFA: stl file.

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 10:19 AM, Andras Lasso <[hidden email]> wrote:

> Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Usually you cannot segment vessels by simple thresholding. It’s normal that opacified vessels have the same intensity as bones or other tissues.

 

You can segment the vessel manually: Find a reasonably good threshold range using the threshold effect and click “Use for masking” instead of “Apply”. Then use the paint tool, select “Sphere brush” option, and follow and paint the vessels.

 

You can also try vessel enhancement filter in VMTK extension to enhance vessels and suppress other structures. The vesselness-filtered image will mostly just contain vasculature, so you can extract the vessel tree in the segment editor automatically, by simple thresholding.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Viraj Belekar
Sent: March 28, 2017 0:32
To: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hi Miten,

 

Can you help me in identifying the threshold range for portal veins? Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Thanks a lot!

 

Regards

Viraj Belekar

 

On Tue, Mar 21, 2017 at 5:29 PM, Patel, Miten <[hidden email]> wrote:

Hi Viraj,

 

Following link and attached tutorial referenced on the web page show the steps to generate an STL from DICOM files.

 

 

The tutorial uses the nightly build rather than 4.6 released version. I've tried it with nightly build from around 15 Mar and it worked fine.

 

The tutorial has extra bits of adding a model etc which you can ignore.

 

We are due to perform the same task for carotid arteries ie STL generation and also centreline extraction for creating geometry for finite element analysis.

 

Would appreciate liaising with you on these steps as looks like we are working on similar tasks.

 

Miten



-------- Original message --------
From: Viraj Belekar <[hidden email]>
Date: 21/03/2017 11:24 (GMT+00:00)
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Making 3D .stl model from DICOM files

Hello everyone,

 

Is there a proper tutorial which addresses making 3D models in .stl format from DICOM files? I want to make a 3D model of portal vein system from DICOM files. Also what should be the threshold range for veins?

 

Thanks and Regards

Viraj Belekar

 

 

 



_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Making 3D .stl model from DICOM files

Viraj Belekar
Hello,

1) Again, I had downloaded the Nightly Build version and VMTK is not available through the extension manager for it. Please help me in this regard.

2) I tried to build Slicer through source code and also compiled VMTK through source code. Is there any tutorial for 'Vesselness filter'? From what I tried to do, the source code version of vmtk is not working. Please help!

3) Without using 'Vesselness filter', I tried to extract the vein stl file. But the model is again with fused ends. I want the model to be hollow and without fused(closed) ends. Please help!

Thank you very much.

Best Regards
Viraj

On Thu, Mar 30, 2017 at 11:20 AM, Viraj Belekar <[hidden email]> wrote:
Hi Mr. Andras,

I had downloaded the Nightly Build version and VMTK is not available through the extension manager for it.

On Wed, Mar 29, 2017 at 6:24 PM, Andras Lasso <[hidden email]> wrote:

VMTK is available now through the extension manager. There is no need to manually download or build anything.

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 29, 2017 3:32


To: Andras Lasso <[hidden email]>
Cc: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello,

 

How do I install VMTK extension as mentioned in the link provided by you? I am following steps on the mentioned here: https://www.slicer.org/wiki/Slicer4:VMTK#Installation

 

But I need a password to use this command: git clone https://haehn@.../haehn/VMTK-in-3D-Slicer.git

 

Thanks

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 5:39 PM, Andras Lasso <[hidden email]> wrote:

To create hollow vessel models, use margin and logical operator effects as described here:

http://slicer-users.65878.n3.nabble.com/Hollow-model-tp4031241p4031242.html

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 28, 2017 7:45
To: Andras Lasso <[hidden email]>
Cc: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Yes the model should be hollow like a tube as I want to analyse internal flow. If you see the stl file, the ends of the vein are fused which I don't want.

 

 

On Tue, 28 Mar 2017 at 5:10 PM, Andras Lasso <[hidden email]> wrote:

Would you like to make the model hollow (like a tube)?

 

Andras

 

From: [hidden email]
Sent: Tuesday, March 28, 2017 2:12 AM
To: [hidden email]
Cc: [hidden email]; [hidden email]


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

Hello Mr. Andras,

 

By using the technique described by you. I am able to extract a few blood vessel models. The thing is I need to do blood flow analysis using these models. For that I want the end of these veins to be open so that I can define a different surface on these open ends as inlet or outlet. Can you please help?

 

PFA: stl file.

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 10:19 AM, Andras Lasso <[hidden email]> wrote:

> Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Usually you cannot segment vessels by simple thresholding. It’s normal that opacified vessels have the same intensity as bones or other tissues.

 

You can segment the vessel manually: Find a reasonably good threshold range using the threshold effect and click “Use for masking” instead of “Apply”. Then use the paint tool, select “Sphere brush” option, and follow and paint the vessels.

 

You can also try vessel enhancement filter in VMTK extension to enhance vessels and suppress other structures. The vesselness-filtered image will mostly just contain vasculature, so you can extract the vessel tree in the segment editor automatically, by simple thresholding.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Viraj Belekar
Sent: March 28, 2017 0:32
To: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hi Miten,

 

Can you help me in identifying the threshold range for portal veins? Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Thanks a lot!

 

Regards

Viraj Belekar

 

On Tue, Mar 21, 2017 at 5:29 PM, Patel, Miten <[hidden email]> wrote:

Hi Viraj,

 

Following link and attached tutorial referenced on the web page show the steps to generate an STL from DICOM files.

 

 

The tutorial uses the nightly build rather than 4.6 released version. I've tried it with nightly build from around 15 Mar and it worked fine.

 

The tutorial has extra bits of adding a model etc which you can ignore.

 

We are due to perform the same task for carotid arteries ie STL generation and also centreline extraction for creating geometry for finite element analysis.

 

Would appreciate liaising with you on these steps as looks like we are working on similar tasks.

 

Miten



-------- Original message --------
From: Viraj Belekar <[hidden email]>
Date: 21/03/2017 11:24 (GMT+00:00)
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Making 3D .stl model from DICOM files

Hello everyone,

 

Is there a proper tutorial which addresses making 3D models in .stl format from DICOM files? I want to make a 3D model of portal vein system from DICOM files. Also what should be the threshold range for veins?

 

Thanks and Regards

Viraj Belekar

 

 

 



_______________________________________________
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


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Making 3D .stl model from DICOM files

Csaba Pinter-2

Hi,

 

According to the dashboard [1], VMTK is available for Mac and Windows (but on Linux there is a persistent build failure apparently). If you install this nightly, then it should be available in extension manager

Windows: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-03-29-win-amd64.exe&checksum=dbcdf1a2ccc8d4298941a31f465faef7

MacOS: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-03-29-macosx-amd64.dmg&checksum=d9176594da4615699f6d36b845b071c6

 

If it’s not in extension manager somehow, then you can install it using the wrench icon in the top left corner of extension manager by choosing this package:

Windows: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=25892-win-amd64-SlicerExtension-VMTK-gite056805-2016-10-21.zip&checksum=24d94af9711ca9280593a8632e65ab56

Mac: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=25892-macosx-amd64-SlicerExtension-VMTK-gite056805-2016-10-21.tar.gz&checksum=333453dca8a67ee281136dd712ec899e

 

Of course if you’re confident in your custom builds, then this will not improve anything, but in case you suspect problems there, it might.

 

csaba

 

[1] http://slicer.cdash.org/index.php?project=Slicer4&filtercount=1&showfilters=1&field1=label&compare1=63&value1=VMTK

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Viraj Belekar
Sent: Thursday, March 30, 2017 07:51
To: Andras Lasso <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Patel, Miten <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello,

 

1) Again, I had downloaded the Nightly Build version and VMTK is not available through the extension manager for it. Please help me in this regard.

 

2) I tried to build Slicer through source code and also compiled VMTK through source code. Is there any tutorial for 'Vesselness filter'? From what I tried to do, the source code version of vmtk is not working. Please help!

 

3) Without using 'Vesselness filter', I tried to extract the vein stl file. But the model is again with fused ends. I want the model to be hollow and without fused(closed) ends. Please help!

 

Thank you very much.

 

Best Regards

Viraj

 

On Thu, Mar 30, 2017 at 11:20 AM, Viraj Belekar <[hidden email]> wrote:

Hi Mr. Andras,

 

I had downloaded the Nightly Build version and VMTK is not available through the extension manager for it.

 

On Wed, Mar 29, 2017 at 6:24 PM, Andras Lasso <[hidden email]> wrote:

VMTK is available now through the extension manager. There is no need to manually download or build anything.

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 29, 2017 3:32


To: Andras Lasso <[hidden email]>
Cc: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello,

 

How do I install VMTK extension as mentioned in the link provided by you? I am following steps on the mentioned here: https://www.slicer.org/wiki/Slicer4:VMTK#Installation

 

But I need a password to use this command: git clone https://haehn@.../haehn/VMTK-in-3D-Slicer.git

 

Thanks

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 5:39 PM, Andras Lasso <[hidden email]> wrote:

To create hollow vessel models, use margin and logical operator effects as described here:

http://slicer-users.65878.n3.nabble.com/Hollow-model-tp4031241p4031242.html

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 28, 2017 7:45
To: Andras Lasso <
[hidden email]>
Cc: Patel, Miten <
[hidden email]>; SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Yes the model should be hollow like a tube as I want to analyse internal flow. If you see the stl file, the ends of the vein are fused which I don't want.

 

 

On Tue, 28 Mar 2017 at 5:10 PM, Andras Lasso <[hidden email]> wrote:

Would you like to make the model hollow (like a tube)?

 

Andras

 

From: [hidden email]
Sent: Tuesday, March 28, 2017 2:12 AM
To: [hidden email]
Cc: [hidden email]; [hidden email]


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

Hello Mr. Andras,

 

By using the technique described by you. I am able to extract a few blood vessel models. The thing is I need to do blood flow analysis using these models. For that I want the end of these veins to be open so that I can define a different surface on these open ends as inlet or outlet. Can you please help?

 

PFA: stl file.

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 10:19 AM, Andras Lasso <[hidden email]> wrote:

> Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Usually you cannot segment vessels by simple thresholding. It’s normal that opacified vessels have the same intensity as bones or other tissues.

 

You can segment the vessel manually: Find a reasonably good threshold range using the threshold effect and click “Use for masking” instead of “Apply”. Then use the paint tool, select “Sphere brush” option, and follow and paint the vessels.

 

You can also try vessel enhancement filter in VMTK extension to enhance vessels and suppress other structures. The vesselness-filtered image will mostly just contain vasculature, so you can extract the vessel tree in the segment editor automatically, by simple thresholding.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Viraj Belekar
Sent: March 28, 2017 0:32
To: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hi Miten,

 

Can you help me in identifying the threshold range for portal veins? Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Thanks a lot!

 

Regards

Viraj Belekar

 

On Tue, Mar 21, 2017 at 5:29 PM, Patel, Miten <[hidden email]> wrote:

Hi Viraj,

 

Following link and attached tutorial referenced on the web page show the steps to generate an STL from DICOM files.

 

 

The tutorial uses the nightly build rather than 4.6 released version. I've tried it with nightly build from around 15 Mar and it worked fine.

 

The tutorial has extra bits of adding a model etc which you can ignore.

 

We are due to perform the same task for carotid arteries ie STL generation and also centreline extraction for creating geometry for finite element analysis.

 

Would appreciate liaising with you on these steps as looks like we are working on similar tasks.

 

Miten



-------- Original message --------
From: Viraj Belekar <[hidden email]>
Date: 21/03/2017 11:24 (GMT+00:00)
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Making 3D .stl model from DICOM files

Hello everyone,

 

Is there a proper tutorial which addresses making 3D models in .stl format from DICOM files? I want to make a 3D model of portal vein system from DICOM files. Also what should be the threshold range for veins?

 

Thanks and Regards

Viraj Belekar

 

 

 

 


_______________________________________________
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

 


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Making 3D .stl model from DICOM files

Andras Lasso-2
In reply to this post by Viraj Belekar

The VMTK build error was the usual problem of not setting the C compiler in the external project. I’ve pushed a fix, VMTK extension should appear for linux tomorrow.

 

Andras

 

From: Csaba Pinter
Sent: March 30, 2017 8:54
To: Viraj Belekar <[hidden email]>; Andras Lasso <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Patel, Miten <[hidden email]>
Subject: RE: [slicer-users] Making 3D .stl model from DICOM files

 

Hi,

 

According to the dashboard [1], VMTK is available for Mac and Windows (but on Linux there is a persistent build failure apparently). If you install this nightly, then it should be available in extension manager

Windows: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-03-29-win-amd64.exe&checksum=dbcdf1a2ccc8d4298941a31f465faef7

MacOS: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-03-29-macosx-amd64.dmg&checksum=d9176594da4615699f6d36b845b071c6

 

If it’s not in extension manager somehow, then you can install it using the wrench icon in the top left corner of extension manager by choosing this package:

Windows: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=25892-win-amd64-SlicerExtension-VMTK-gite056805-2016-10-21.zip&checksum=24d94af9711ca9280593a8632e65ab56

Mac: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=25892-macosx-amd64-SlicerExtension-VMTK-gite056805-2016-10-21.tar.gz&checksum=333453dca8a67ee281136dd712ec899e

 

Of course if you’re confident in your custom builds, then this will not improve anything, but in case you suspect problems there, it might.

 

csaba

 

[1] http://slicer.cdash.org/index.php?project=Slicer4&filtercount=1&showfilters=1&field1=label&compare1=63&value1=VMTK

 

From: slicer-users [[hidden email]] On Behalf Of Viraj Belekar
Sent: Thursday, March 30, 2017 07:51
To: Andras Lasso <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Patel, Miten <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello,

 

1) Again, I had downloaded the Nightly Build version and VMTK is not available through the extension manager for it. Please help me in this regard.

 

2) I tried to build Slicer through source code and also compiled VMTK through source code. Is there any tutorial for 'Vesselness filter'? From what I tried to do, the source code version of vmtk is not working. Please help!

 

3) Without using 'Vesselness filter', I tried to extract the vein stl file. But the model is again with fused ends. I want the model to be hollow and without fused(closed) ends. Please help!

 

Thank you very much.

 

Best Regards

Viraj

 

On Thu, Mar 30, 2017 at 11:20 AM, Viraj Belekar <[hidden email]> wrote:

Hi Mr. Andras,

 

I had downloaded the Nightly Build version and VMTK is not available through the extension manager for it.

 

On Wed, Mar 29, 2017 at 6:24 PM, Andras Lasso <[hidden email]> wrote:

VMTK is available now through the extension manager. There is no need to manually download or build anything.

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 29, 2017 3:32


To: Andras Lasso <[hidden email]>
Cc: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello,

 

How do I install VMTK extension as mentioned in the link provided by you? I am following steps on the mentioned here: https://www.slicer.org/wiki/Slicer4:VMTK#Installation

 

But I need a password to use this command: git clone https://haehn@.../haehn/VMTK-in-3D-Slicer.git

 

Thanks

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 5:39 PM, Andras Lasso <[hidden email]> wrote:

To create hollow vessel models, use margin and logical operator effects as described here:

http://slicer-users.65878.n3.nabble.com/Hollow-model-tp4031241p4031242.html

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 28, 2017 7:45
To: Andras Lasso <
[hidden email]>
Cc: Patel, Miten <
[hidden email]>; SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Yes the model should be hollow like a tube as I want to analyse internal flow. If you see the stl file, the ends of the vein are fused which I don't want.

 

 

On Tue, 28 Mar 2017 at 5:10 PM, Andras Lasso <[hidden email]> wrote:

Would you like to make the model hollow (like a tube)?

 

Andras

 

From: [hidden email]
Sent: Tuesday, March 28, 2017 2:12 AM
To: [hidden email]
Cc: [hidden email]; [hidden email]


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

Hello Mr. Andras,

 

By using the technique described by you. I am able to extract a few blood vessel models. The thing is I need to do blood flow analysis using these models. For that I want the end of these veins to be open so that I can define a different surface on these open ends as inlet or outlet. Can you please help?

 

PFA: stl file.

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 10:19 AM, Andras Lasso <[hidden email]> wrote:

> Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Usually you cannot segment vessels by simple thresholding. It’s normal that opacified vessels have the same intensity as bones or other tissues.

 

You can segment the vessel manually: Find a reasonably good threshold range using the threshold effect and click “Use for masking” instead of “Apply”. Then use the paint tool, select “Sphere brush” option, and follow and paint the vessels.

 

You can also try vessel enhancement filter in VMTK extension to enhance vessels and suppress other structures. The vesselness-filtered image will mostly just contain vasculature, so you can extract the vessel tree in the segment editor automatically, by simple thresholding.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Viraj Belekar
Sent: March 28, 2017 0:32
To: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hi Miten,

 

Can you help me in identifying the threshold range for portal veins? Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Thanks a lot!

 

Regards

Viraj Belekar

 

On Tue, Mar 21, 2017 at 5:29 PM, Patel, Miten <[hidden email]> wrote:

Hi Viraj,

 

Following link and attached tutorial referenced on the web page show the steps to generate an STL from DICOM files.

 

 

The tutorial uses the nightly build rather than 4.6 released version. I've tried it with nightly build from around 15 Mar and it worked fine.

 

The tutorial has extra bits of adding a model etc which you can ignore.

 

We are due to perform the same task for carotid arteries ie STL generation and also centreline extraction for creating geometry for finite element analysis.

 

Would appreciate liaising with you on these steps as looks like we are working on similar tasks.

 

Miten



-------- Original message --------
From: Viraj Belekar <[hidden email]>
Date: 21/03/2017 11:24 (GMT+00:00)
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Making 3D .stl model from DICOM files

Hello everyone,

 

Is there a proper tutorial which addresses making 3D models in .stl format from DICOM files? I want to make a 3D model of portal vein system from DICOM files. Also what should be the threshold range for veins?

 

Thanks and Regards

Viraj Belekar

 

 

 

 


_______________________________________________
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

 


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Making 3D .stl model from DICOM files

Viraj Belekar
In reply to this post by Viraj Belekar
Hello everyone,

1) I don't know why vesselness filter isn't working for the LINUX version. When I select a Fiducial using mouse, similar intensity regions get highlighted but when I follow the later steps using Segment Editor and click on 'Create Surface', a surface which includes in the Fiducial point is created and nothing else.

2) URGENT! I created a hollow surface of blood vessel by following the steps on this link. I think I did it correctly this time(PFA: stl file). The problem which I want to resolve is that the hollow surface contains fused ends. I need a model with open ends to apply appropriate boundary conditions. Can anyone help in this regard?

Thanks and Regards
Viraj Belekar

On Thu, Mar 30, 2017 at 7:15 PM, Andras Lasso <[hidden email]> wrote:

The VMTK build error was the usual problem of not setting the C compiler in the external project. I’ve pushed a fix, VMTK extension should appear for linux tomorrow.

 

Andras

 

From: Csaba Pinter
Sent: March 30, 2017 8:54
To: Viraj Belekar <[hidden email]>; Andras Lasso <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Patel, Miten <[hidden email]>
Subject: RE: [slicer-users] Making 3D .stl model from DICOM files

 

Hi,

 

According to the dashboard [1], VMTK is available for Mac and Windows (but on Linux there is a persistent build failure apparently). If you install this nightly, then it should be available in extension manager

Windows: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-03-29-win-amd64.exe&checksum=dbcdf1a2ccc8d4298941a31f465faef7

MacOS: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-03-29-macosx-amd64.dmg&checksum=d9176594da4615699f6d36b845b071c6

 

If it’s not in extension manager somehow, then you can install it using the wrench icon in the top left corner of extension manager by choosing this package:

Windows: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=25892-win-amd64-SlicerExtension-VMTK-gite056805-2016-10-21.zip&checksum=24d94af9711ca9280593a8632e65ab56

Mac: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=25892-macosx-amd64-SlicerExtension-VMTK-gite056805-2016-10-21.tar.gz&checksum=333453dca8a67ee281136dd712ec899e

 

Of course if you’re confident in your custom builds, then this will not improve anything, but in case you suspect problems there, it might.

 

csaba

 

[1] http://slicer.cdash.org/index.php?project=Slicer4&filtercount=1&showfilters=1&field1=label&compare1=63&value1=VMTK

 

From: slicer-users [[hidden email]] On Behalf Of Viraj Belekar
Sent: Thursday, March 30, 2017 07:51
To: Andras Lasso <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Patel, Miten <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello,

 

1) Again, I had downloaded the Nightly Build version and VMTK is not available through the extension manager for it. Please help me in this regard.

 

2) I tried to build Slicer through source code and also compiled VMTK through source code. Is there any tutorial for 'Vesselness filter'? From what I tried to do, the source code version of vmtk is not working. Please help!

 

3) Without using 'Vesselness filter', I tried to extract the vein stl file. But the model is again with fused ends. I want the model to be hollow and without fused(closed) ends. Please help!

 

Thank you very much.

 

Best Regards

Viraj

 

On Thu, Mar 30, 2017 at 11:20 AM, Viraj Belekar <[hidden email]> wrote:

Hi Mr. Andras,

 

I had downloaded the Nightly Build version and VMTK is not available through the extension manager for it.

 

On Wed, Mar 29, 2017 at 6:24 PM, Andras Lasso <[hidden email]> wrote:

VMTK is available now through the extension manager. There is no need to manually download or build anything.

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 29, 2017 3:32


To: Andras Lasso <[hidden email]>
Cc: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello,

 

How do I install VMTK extension as mentioned in the link provided by you? I am following steps on the mentioned here: https://www.slicer.org/wiki/Slicer4:VMTK#Installation

 

But I need a password to use this command: git clone https://haehn@.../haehn/VMTK-in-3D-Slicer.git

 

Thanks

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 5:39 PM, Andras Lasso <[hidden email]> wrote:

To create hollow vessel models, use margin and logical operator effects as described here:

http://slicer-users.65878.n3.nabble.com/Hollow-model-tp4031241p4031242.html

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 28, 2017 7:45
To: Andras Lasso <
[hidden email]>
Cc: Patel, Miten <
[hidden email]>; SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Yes the model should be hollow like a tube as I want to analyse internal flow. If you see the stl file, the ends of the vein are fused which I don't want.

 

 

On Tue, 28 Mar 2017 at 5:10 PM, Andras Lasso <[hidden email]> wrote:

Would you like to make the model hollow (like a tube)?

 

Andras

 

From: [hidden email]
Sent: Tuesday, March 28, 2017 2:12 AM
To: [hidden email]
Cc: [hidden email]; [hidden email]


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

Hello Mr. Andras,

 

By using the technique described by you. I am able to extract a few blood vessel models. The thing is I need to do blood flow analysis using these models. For that I want the end of these veins to be open so that I can define a different surface on these open ends as inlet or outlet. Can you please help?

 

PFA: stl file.

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 10:19 AM, Andras Lasso <[hidden email]> wrote:

> Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Usually you cannot segment vessels by simple thresholding. It’s normal that opacified vessels have the same intensity as bones or other tissues.

 

You can segment the vessel manually: Find a reasonably good threshold range using the threshold effect and click “Use for masking” instead of “Apply”. Then use the paint tool, select “Sphere brush” option, and follow and paint the vessels.

 

You can also try vessel enhancement filter in VMTK extension to enhance vessels and suppress other structures. The vesselness-filtered image will mostly just contain vasculature, so you can extract the vessel tree in the segment editor automatically, by simple thresholding.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Viraj Belekar
Sent: March 28, 2017 0:32
To: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hi Miten,

 

Can you help me in identifying the threshold range for portal veins? Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Thanks a lot!

 

Regards

Viraj Belekar

 

On Tue, Mar 21, 2017 at 5:29 PM, Patel, Miten <[hidden email]> wrote:

Hi Viraj,

 

Following link and attached tutorial referenced on the web page show the steps to generate an STL from DICOM files.

 

 

The tutorial uses the nightly build rather than 4.6 released version. I've tried it with nightly build from around 15 Mar and it worked fine.

 

The tutorial has extra bits of adding a model etc which you can ignore.

 

We are due to perform the same task for carotid arteries ie STL generation and also centreline extraction for creating geometry for finite element analysis.

 

Would appreciate liaising with you on these steps as looks like we are working on similar tasks.

 

Miten



-------- Original message --------
From: Viraj Belekar <[hidden email]>
Date: 21/03/2017 11:24 (GMT+00:00)
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Making 3D .stl model from DICOM files

Hello everyone,

 

Is there a proper tutorial which addresses making 3D models in .stl format from DICOM files? I want to make a 3D model of portal vein system from DICOM files. Also what should be the threshold range for veins?

 

Thanks and Regards

Viraj Belekar

 

 

 

 


_______________________________________________
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

 



_______________________________________________
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

Segment_3.stl (150K) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: Making 3D .stl model from DICOM files

Csaba Pinter-2
In reply to this post by Viraj Belekar

1) Are you absolutely sure that you have a ‘segmentation’ node and not another type? You can only use Segment Editor with segmentations. Can you go to subject hierarchy and make a screenshot for us to see what you have?

2) You can use the Scissors tool (or simply the Eraser) in Segment Editor to cut off the cap

 

csaba

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: Monday, April 3, 2017 03:24
To: Andras Lasso <[hidden email]>
Cc: Csaba Pinter <[hidden email]>; SPL Slicer Users <[hidden email]>; Patel, Miten <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello everyone,

 

1) I don't know why vesselness filter isn't working for the LINUX version. When I select a Fiducial using mouse, similar intensity regions get highlighted but when I follow the later steps using Segment Editor and click on 'Create Surface', a surface which includes in the Fiducial point is created and nothing else.

 

2) URGENT! I created a hollow surface of blood vessel by following the steps on this link. I think I did it correctly this time(PFA: stl file). The problem which I want to resolve is that the hollow surface contains fused ends. I need a model with open ends to apply appropriate boundary conditions. Can anyone help in this regard?

 

Thanks and Regards

Viraj Belekar

 

On Thu, Mar 30, 2017 at 7:15 PM, Andras Lasso <[hidden email]> wrote:

The VMTK build error was the usual problem of not setting the C compiler in the external project. I’ve pushed a fix, VMTK extension should appear for linux tomorrow.

 

Andras

 

From: Csaba Pinter
Sent: March 30, 2017 8:54
To: Viraj Belekar <[hidden email]>; Andras Lasso <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Patel, Miten <[hidden email]>
Subject: RE: [slicer-users] Making 3D .stl model from DICOM files

 

Hi,

 

According to the dashboard [1], VMTK is available for Mac and Windows (but on Linux there is a persistent build failure apparently). If you install this nightly, then it should be available in extension manager

Windows: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-03-29-win-amd64.exe&checksum=dbcdf1a2ccc8d4298941a31f465faef7

MacOS: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-03-29-macosx-amd64.dmg&checksum=d9176594da4615699f6d36b845b071c6

 

If it’s not in extension manager somehow, then you can install it using the wrench icon in the top left corner of extension manager by choosing this package:

Windows: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=25892-win-amd64-SlicerExtension-VMTK-gite056805-2016-10-21.zip&checksum=24d94af9711ca9280593a8632e65ab56

Mac: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=25892-macosx-amd64-SlicerExtension-VMTK-gite056805-2016-10-21.tar.gz&checksum=333453dca8a67ee281136dd712ec899e

 

Of course if you’re confident in your custom builds, then this will not improve anything, but in case you suspect problems there, it might.

 

csaba

 

[1] http://slicer.cdash.org/index.php?project=Slicer4&filtercount=1&showfilters=1&field1=label&compare1=63&value1=VMTK

 

From: slicer-users [[hidden email]] On Behalf Of Viraj Belekar
Sent: Thursday, March 30, 2017 07:51
To: Andras Lasso <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Patel, Miten <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello,

 

1) Again, I had downloaded the Nightly Build version and VMTK is not available through the extension manager for it. Please help me in this regard.

 

2) I tried to build Slicer through source code and also compiled VMTK through source code. Is there any tutorial for 'Vesselness filter'? From what I tried to do, the source code version of vmtk is not working. Please help!

 

3) Without using 'Vesselness filter', I tried to extract the vein stl file. But the model is again with fused ends. I want the model to be hollow and without fused(closed) ends. Please help!

 

Thank you very much.

 

Best Regards

Viraj

 

On Thu, Mar 30, 2017 at 11:20 AM, Viraj Belekar <[hidden email]> wrote:

Hi Mr. Andras,

 

I had downloaded the Nightly Build version and VMTK is not available through the extension manager for it.

 

On Wed, Mar 29, 2017 at 6:24 PM, Andras Lasso <[hidden email]> wrote:

VMTK is available now through the extension manager. There is no need to manually download or build anything.

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 29, 2017 3:32


To: Andras Lasso <[hidden email]>
Cc: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello,

 

How do I install VMTK extension as mentioned in the link provided by you? I am following steps on the mentioned here: https://www.slicer.org/wiki/Slicer4:VMTK#Installation

 

But I need a password to use this command: git clone https://haehn@.../haehn/VMTK-in-3D-Slicer.git

 

Thanks

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 5:39 PM, Andras Lasso <[hidden email]> wrote:

To create hollow vessel models, use margin and logical operator effects as described here:

http://slicer-users.65878.n3.nabble.com/Hollow-model-tp4031241p4031242.html

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 28, 2017 7:45
To: Andras Lasso <
[hidden email]>
Cc: Patel, Miten <
[hidden email]>; SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Yes the model should be hollow like a tube as I want to analyse internal flow. If you see the stl file, the ends of the vein are fused which I don't want.

 

 

On Tue, 28 Mar 2017 at 5:10 PM, Andras Lasso <[hidden email]> wrote:

Would you like to make the model hollow (like a tube)?

 

Andras

 

From: [hidden email]
Sent: Tuesday, March 28, 2017 2:12 AM
To: [hidden email]
Cc: [hidden email]; [hidden email]


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

Hello Mr. Andras,

 

By using the technique described by you. I am able to extract a few blood vessel models. The thing is I need to do blood flow analysis using these models. For that I want the end of these veins to be open so that I can define a different surface on these open ends as inlet or outlet. Can you please help?

 

PFA: stl file.

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 10:19 AM, Andras Lasso <[hidden email]> wrote:

> Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Usually you cannot segment vessels by simple thresholding. It’s normal that opacified vessels have the same intensity as bones or other tissues.

 

You can segment the vessel manually: Find a reasonably good threshold range using the threshold effect and click “Use for masking” instead of “Apply”. Then use the paint tool, select “Sphere brush” option, and follow and paint the vessels.

 

You can also try vessel enhancement filter in VMTK extension to enhance vessels and suppress other structures. The vesselness-filtered image will mostly just contain vasculature, so you can extract the vessel tree in the segment editor automatically, by simple thresholding.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Viraj Belekar
Sent: March 28, 2017 0:32
To: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hi Miten,

 

Can you help me in identifying the threshold range for portal veins? Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Thanks a lot!

 

Regards

Viraj Belekar

 

On Tue, Mar 21, 2017 at 5:29 PM, Patel, Miten <[hidden email]> wrote:

Hi Viraj,

 

Following link and attached tutorial referenced on the web page show the steps to generate an STL from DICOM files.

 

 

The tutorial uses the nightly build rather than 4.6 released version. I've tried it with nightly build from around 15 Mar and it worked fine.

 

The tutorial has extra bits of adding a model etc which you can ignore.

 

We are due to perform the same task for carotid arteries ie STL generation and also centreline extraction for creating geometry for finite element analysis.

 

Would appreciate liaising with you on these steps as looks like we are working on similar tasks.

 

Miten



-------- Original message --------
From: Viraj Belekar <[hidden email]>
Date: 21/03/2017 11:24 (GMT+00:00)
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Making 3D .stl model from DICOM files

Hello everyone,

 

Is there a proper tutorial which addresses making 3D models in .stl format from DICOM files? I want to make a 3D model of portal vein system from DICOM files. Also what should be the threshold range for veins?

 

Thanks and Regards

Viraj Belekar

 

 

 

 


_______________________________________________
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

 

 


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Making 3D .stl model from DICOM files

Viraj Belekar
In reply to this post by Viraj Belekar
1) I will send you the screenshot today itself.


2) The scissors tool isnt working with the hollow surface which I create.


On Mon, 3 Apr 2017 at 6:55 PM, Csaba Pinter <[hidden email]> wrote:

1) Are you absolutely sure that you have a ‘segmentation’ node and not another type? You can only use Segment Editor with segmentations. Can you go to subject hierarchy and make a screenshot for us to see what you have?

2) You can use the Scissors tool (or simply the Eraser) in Segment Editor to cut off the cap

 

csaba

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: Monday, April 3, 2017 03:24
To: Andras Lasso <[hidden email]>
Cc: Csaba Pinter <[hidden email]>; SPL Slicer Users <[hidden email]>; Patel, Miten <[hidden email]>


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello everyone,

 

1) I don't know why vesselness filter isn't working for the LINUX version. When I select a Fiducial using mouse, similar intensity regions get highlighted but when I follow the later steps using Segment Editor and click on 'Create Surface', a surface which includes in the Fiducial point is created and nothing else.

 

2) URGENT! I created a hollow surface of blood vessel by following the steps on this link. I think I did it correctly this time(PFA: stl file). The problem which I want to resolve is that the hollow surface contains fused ends. I need a model with open ends to apply appropriate boundary conditions. Can anyone help in this regard?

 

Thanks and Regards

Viraj Belekar

 

On Thu, Mar 30, 2017 at 7:15 PM, Andras Lasso <[hidden email]> wrote:

The VMTK build error was the usual problem of not setting the C compiler in the external project. I’ve pushed a fix, VMTK extension should appear for linux tomorrow.

 

Andras

 

From: Csaba Pinter
Sent: March 30, 2017 8:54
To: Viraj Belekar <[hidden email]>; Andras Lasso <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Patel, Miten <[hidden email]>
Subject: RE: [slicer-users] Making 3D .stl model from DICOM files

 

Hi,

 

According to the dashboard [1], VMTK is available for Mac and Windows (but on Linux there is a persistent build failure apparently). If you install this nightly, then it should be available in extension manager

Windows: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-03-29-win-amd64.exe&checksum=dbcdf1a2ccc8d4298941a31f465faef7

MacOS: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-03-29-macosx-amd64.dmg&checksum=d9176594da4615699f6d36b845b071c6

 

If it’s not in extension manager somehow, then you can install it using the wrench icon in the top left corner of extension manager by choosing this package:

Windows: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=25892-win-amd64-SlicerExtension-VMTK-gite056805-2016-10-21.zip&checksum=24d94af9711ca9280593a8632e65ab56

Mac: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=25892-macosx-amd64-SlicerExtension-VMTK-gite056805-2016-10-21.tar.gz&checksum=333453dca8a67ee281136dd712ec899e

 

Of course if you’re confident in your custom builds, then this will not improve anything, but in case you suspect problems there, it might.

 

csaba

 

[1] http://slicer.cdash.org/index.php?project=Slicer4&filtercount=1&showfilters=1&field1=label&compare1=63&value1=VMTK

 

From: slicer-users [[hidden email]] On Behalf Of Viraj Belekar
Sent: Thursday, March 30, 2017 07:51
To: Andras Lasso <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Patel, Miten <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello,

 

1) Again, I had downloaded the Nightly Build version and VMTK is not available through the extension manager for it. Please help me in this regard.

 

2) I tried to build Slicer through source code and also compiled VMTK through source code. Is there any tutorial for 'Vesselness filter'? From what I tried to do, the source code version of vmtk is not working. Please help!

 

3) Without using 'Vesselness filter', I tried to extract the vein stl file. But the model is again with fused ends. I want the model to be hollow and without fused(closed) ends. Please help!

 

Thank you very much.

 

Best Regards

Viraj

 

On Thu, Mar 30, 2017 at 11:20 AM, Viraj Belekar <[hidden email]> wrote:

Hi Mr. Andras,

 

I had downloaded the Nightly Build version and VMTK is not available through the extension manager for it.

 

On Wed, Mar 29, 2017 at 6:24 PM, Andras Lasso <[hidden email]> wrote:

VMTK is available now through the extension manager. There is no need to manually download or build anything.

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 29, 2017 3:32


To: Andras Lasso <[hidden email]>
Cc: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello,

 

How do I install VMTK extension as mentioned in the link provided by you? I am following steps on the mentioned here: https://www.slicer.org/wiki/Slicer4:VMTK#Installation

 

But I need a password to use this command: git clone https://haehn@.../haehn/VMTK-in-3D-Slicer.git

 

Thanks

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 5:39 PM, Andras Lasso <[hidden email]> wrote:

To create hollow vessel models, use margin and logical operator effects as described here:

http://slicer-users.65878.n3.nabble.com/Hollow-model-tp4031241p4031242.html

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 28, 2017 7:45
To: Andras Lasso <
[hidden email]>
Cc: Patel, Miten <
[hidden email]>; SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Yes the model should be hollow like a tube as I want to analyse internal flow. If you see the stl file, the ends of the vein are fused which I don't want.

 

 

On Tue, 28 Mar 2017 at 5:10 PM, Andras Lasso <[hidden email]> wrote:

Would you like to make the model hollow (like a tube)?

 

Andras

 

From: [hidden email]
Sent: Tuesday, March 28, 2017 2:12 AM
To: [hidden email]
Cc: [hidden email]; [hidden email]


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

Hello Mr. Andras,

 

By using the technique described by you. I am able to extract a few blood vessel models. The thing is I need to do blood flow analysis using these models. For that I want the end of these veins to be open so that I can define a different surface on these open ends as inlet or outlet. Can you please help?

 

PFA: stl file.

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 10:19 AM, Andras Lasso <[hidden email]> wrote:

> Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Usually you cannot segment vessels by simple thresholding. It’s normal that opacified vessels have the same intensity as bones or other tissues.

 

You can segment the vessel manually: Find a reasonably good threshold range using the threshold effect and click “Use for masking” instead of “Apply”. Then use the paint tool, select “Sphere brush” option, and follow and paint the vessels.

 

You can also try vessel enhancement filter in VMTK extension to enhance vessels and suppress other structures. The vesselness-filtered image will mostly just contain vasculature, so you can extract the vessel tree in the segment editor automatically, by simple thresholding.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Viraj Belekar
Sent: March 28, 2017 0:32
To: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hi Miten,

 

Can you help me in identifying the threshold range for portal veins? Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Thanks a lot!

 

Regards

Viraj Belekar

 

On Tue, Mar 21, 2017 at 5:29 PM, Patel, Miten <[hidden email]> wrote:

Hi Viraj,

 

Following link and attached tutorial referenced on the web page show the steps to generate an STL from DICOM files.

 

 

The tutorial uses the nightly build rather than 4.6 released version. I've tried it with nightly build from around 15 Mar and it worked fine.

 

The tutorial has extra bits of adding a model etc which you can ignore.

 

We are due to perform the same task for carotid arteries ie STL generation and also centreline extraction for creating geometry for finite element analysis.

 

Would appreciate liaising with you on these steps as looks like we are working on similar tasks.

 

Miten



-------- Original message --------
From: Viraj Belekar <[hidden email]>
Date: 21/03/2017 11:24 (GMT+00:00)
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Making 3D .stl model from DICOM files

Hello everyone,

 

Is there a proper tutorial which addresses making 3D models in .stl format from DICOM files? I want to make a 3D model of portal vein system from DICOM files. Also what should be the threshold range for veins?

 

Thanks and Regards

Viraj Belekar

 

 

 

 


_______________________________________________
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

 

 


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Making 3D .stl model from DICOM files

Csaba Pinter-2
In reply to this post by Viraj Belekar

2) A little bit more information could be useful

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: Monday, April 3, 2017 09:35
To: Andras Lasso <[hidden email]>; Csaba Pinter <[hidden email]>
Cc: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

1) I will send you the screenshot today itself.

 

 

2) The scissors tool isnt working with the hollow surface which I create.

 

 

On Mon, 3 Apr 2017 at 6:55 PM, Csaba Pinter <[hidden email]> wrote:

1) Are you absolutely sure that you have a ‘segmentation’ node and not another type? You can only use Segment Editor with segmentations. Can you go to subject hierarchy and make a screenshot for us to see what you have?

2) You can use the Scissors tool (or simply the Eraser) in Segment Editor to cut off the cap

 

csaba

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: Monday, April 3, 2017 03:24
To: Andras Lasso <[hidden email]>
Cc: Csaba Pinter <[hidden email]>; SPL Slicer Users <[hidden email]>; Patel, Miten <[hidden email]>


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello everyone,

 

1) I don't know why vesselness filter isn't working for the LINUX version. When I select a Fiducial using mouse, similar intensity regions get highlighted but when I follow the later steps using Segment Editor and click on 'Create Surface', a surface which includes in the Fiducial point is created and nothing else.

 

2) URGENT! I created a hollow surface of blood vessel by following the steps on this link. I think I did it correctly this time(PFA: stl file). The problem which I want to resolve is that the hollow surface contains fused ends. I need a model with open ends to apply appropriate boundary conditions. Can anyone help in this regard?

 

Thanks and Regards

Viraj Belekar

 

On Thu, Mar 30, 2017 at 7:15 PM, Andras Lasso <[hidden email]> wrote:

The VMTK build error was the usual problem of not setting the C compiler in the external project. I’ve pushed a fix, VMTK extension should appear for linux tomorrow.

 

Andras

 

From: Csaba Pinter
Sent: March 30, 2017 8:54
To: Viraj Belekar <[hidden email]>; Andras Lasso <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Patel, Miten <[hidden email]>
Subject: RE: [slicer-users] Making 3D .stl model from DICOM files

 

Hi,

 

According to the dashboard [1], VMTK is available for Mac and Windows (but on Linux there is a persistent build failure apparently). If you install this nightly, then it should be available in extension manager

Windows: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-03-29-win-amd64.exe&checksum=dbcdf1a2ccc8d4298941a31f465faef7

MacOS: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-03-29-macosx-amd64.dmg&checksum=d9176594da4615699f6d36b845b071c6

 

If it’s not in extension manager somehow, then you can install it using the wrench icon in the top left corner of extension manager by choosing this package:

Windows: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=25892-win-amd64-SlicerExtension-VMTK-gite056805-2016-10-21.zip&checksum=24d94af9711ca9280593a8632e65ab56

Mac: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=25892-macosx-amd64-SlicerExtension-VMTK-gite056805-2016-10-21.tar.gz&checksum=333453dca8a67ee281136dd712ec899e

 

Of course if you’re confident in your custom builds, then this will not improve anything, but in case you suspect problems there, it might.

 

csaba

 

[1] http://slicer.cdash.org/index.php?project=Slicer4&filtercount=1&showfilters=1&field1=label&compare1=63&value1=VMTK

 

From: slicer-users [[hidden email]] On Behalf Of Viraj Belekar
Sent: Thursday, March 30, 2017 07:51
To: Andras Lasso <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>; Patel, Miten <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello,

 

1) Again, I had downloaded the Nightly Build version and VMTK is not available through the extension manager for it. Please help me in this regard.

 

2) I tried to build Slicer through source code and also compiled VMTK through source code. Is there any tutorial for 'Vesselness filter'? From what I tried to do, the source code version of vmtk is not working. Please help!

 

3) Without using 'Vesselness filter', I tried to extract the vein stl file. But the model is again with fused ends. I want the model to be hollow and without fused(closed) ends. Please help!

 

Thank you very much.

 

Best Regards

Viraj

 

On Thu, Mar 30, 2017 at 11:20 AM, Viraj Belekar <[hidden email]> wrote:

Hi Mr. Andras,

 

I had downloaded the Nightly Build version and VMTK is not available through the extension manager for it.

 

On Wed, Mar 29, 2017 at 6:24 PM, Andras Lasso <[hidden email]> wrote:

VMTK is available now through the extension manager. There is no need to manually download or build anything.

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 29, 2017 3:32


To: Andras Lasso <[hidden email]>
Cc: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello,

 

How do I install VMTK extension as mentioned in the link provided by you? I am following steps on the mentioned here: https://www.slicer.org/wiki/Slicer4:VMTK#Installation

 

But I need a password to use this command: git clone https://haehn@.../haehn/VMTK-in-3D-Slicer.git

 

Thanks

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 5:39 PM, Andras Lasso <[hidden email]> wrote:

To create hollow vessel models, use margin and logical operator effects as described here:

http://slicer-users.65878.n3.nabble.com/Hollow-model-tp4031241p4031242.html

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 28, 2017 7:45
To: Andras Lasso <
[hidden email]>
Cc: Patel, Miten <
[hidden email]>; SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Yes the model should be hollow like a tube as I want to analyse internal flow. If you see the stl file, the ends of the vein are fused which I don't want.

 

 

On Tue, 28 Mar 2017 at 5:10 PM, Andras Lasso <[hidden email]> wrote:

Would you like to make the model hollow (like a tube)?

 

Andras

 

From: [hidden email]
Sent: Tuesday, March 28, 2017 2:12 AM
To: [hidden email]
Cc: [hidden email]; [hidden email]


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

Hello Mr. Andras,

 

By using the technique described by you. I am able to extract a few blood vessel models. The thing is I need to do blood flow analysis using these models. For that I want the end of these veins to be open so that I can define a different surface on these open ends as inlet or outlet. Can you please help?

 

PFA: stl file.

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 10:19 AM, Andras Lasso <[hidden email]> wrote:

> Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Usually you cannot segment vessels by simple thresholding. It’s normal that opacified vessels have the same intensity as bones or other tissues.

 

You can segment the vessel manually: Find a reasonably good threshold range using the threshold effect and click “Use for masking” instead of “Apply”. Then use the paint tool, select “Sphere brush” option, and follow and paint the vessels.

 

You can also try vessel enhancement filter in VMTK extension to enhance vessels and suppress other structures. The vesselness-filtered image will mostly just contain vasculature, so you can extract the vessel tree in the segment editor automatically, by simple thresholding.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Viraj Belekar
Sent: March 28, 2017 0:32
To: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hi Miten,

 

Can you help me in identifying the threshold range for portal veins? Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Thanks a lot!

 

Regards

Viraj Belekar

 

On Tue, Mar 21, 2017 at 5:29 PM, Patel, Miten <[hidden email]> wrote:

Hi Viraj,

 

Following link and attached tutorial referenced on the web page show the steps to generate an STL from DICOM files.

 

 

The tutorial uses the nightly build rather than 4.6 released version. I've tried it with nightly build from around 15 Mar and it worked fine.

 

The tutorial has extra bits of adding a model etc which you can ignore.

 

We are due to perform the same task for carotid arteries ie STL generation and also centreline extraction for creating geometry for finite element analysis.

 

Would appreciate liaising with you on these steps as looks like we are working on similar tasks.

 

Miten



-------- Original message --------
From: Viraj Belekar <[hidden email]>
Date: 21/03/2017 11:24 (GMT+00:00)
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Making 3D .stl model from DICOM files

Hello everyone,

 

Is there a proper tutorial which addresses making 3D models in .stl format from DICOM files? I want to make a 3D model of portal vein system from DICOM files. Also what should be the threshold range for veins?

 

Thanks and Regards

Viraj Belekar

 

 

 

 


_______________________________________________
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

 

 


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Making 3D .stl model from DICOM files

Csaba Pinter-2
In reply to this post by Viraj Belekar

Hi Viraj,

 

Thanks for the video!

 

The main problem is that you select one segment (green), but want to use the scissors and then the eraser on the other one (yellow), see image

https://www.dropbox.com/s/hbg8ill1feb7f40/20170403_ScissorsIssue.png?dl=0

The selected effect always edits the segment that is selected, and as you select another segment, the operation of course doesn’t work.

 

Also:

- The margin for growing is too small, so the wall of the vessel will not be solid

- You don’t actually cut the end of the vessel wall, but the dilated vessel segmentation
(you probably know the above two, but you did decide to include these steps in the video, so I thought I’d mention)

- I’d use the 2D view to use the scissors, to make sure that there are actual voxels involved. If you do it in the 3D view, you may try to cut a quarter voxel, because you don’t see the underlying “master” representation, which is the labelmap. The surface in the 3D view is mostly for navigation and high-level scissor operations, not precision ones like this one

 

csaba

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: Monday, April 3, 2017 13:45
To: Andras Lasso <[hidden email]>; Csaba Pinter <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

​Hello Sirs,

 

Please find the attached file!

 

On Mon, Apr 3, 2017 at 7:18 PM, Andras Lasso <[hidden email]> wrote:

> The scissors tool isntworking with the hollow surface which I create.

 

Please send a screencast (a video that shows what steps you do; not a single screenshot) of your entire segmentation and Slicer application log (menu: Help / Report a bug).

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: April 3, 2017 9:35
To: Andras Lasso <[hidden email]>; Csaba Pinter <[hidden email]>

Cc: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

1) I will send you the screenshot today itself.

 

 

2) The scissors tool isnt working with the hollow surface which I create.

 

 

On Mon, 3 Apr 2017 at 6:55 PM, Csaba Pinter <[hidden email]> wrote:

1) Are you absolutely sure that you have a ‘segmentation’ node and not another type? You can only use Segment Editor with segmentations. Can you go to subject hierarchy and make a screenshot for us to see what you have?

2) You can use the Scissors tool (or simply the Eraser) in Segment Editor to cut off the cap

 

csaba

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: Monday, April 3, 2017 03:24
To: Andras Lasso <
[hidden email]>
Cc: Csaba Pinter <
[hidden email]>; SPL Slicer Users <[hidden email]>; Patel, Miten <[hidden email]>


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello everyone,

 

1) I don't know why vesselness filter isn't working for the LINUX version. When I select a Fiducial using mouse, similar intensity regions get highlighted but when I follow the later steps using Segment Editor and click on 'Create Surface', a surface which includes in the Fiducial point is created and nothing else.

 

2) URGENT! I created a hollow surface of blood vessel by following the steps on this link. I think I did it correctly this time(PFA: stl file). The problem which I want to resolve is that the hollow surface contains fused ends. I need a model with open ends to apply appropriate boundary conditions. Can anyone help in this regard?

 

Thanks and Regards

Viraj Belekar

 

On Thu, Mar 30, 2017 at 7:15 PM, Andras Lasso <[hidden email]> wrote:

The VMTK build error was the usual problem of not setting the C compiler in the external project. I’ve pushed a fix, VMTK extension should appear for linux tomorrow.

 

Andras

 

From: Csaba Pinter
Sent: March 30, 2017 8:54
To: Viraj Belekar <
[hidden email]>; Andras Lasso <[hidden email]>
Cc: SPL Slicer Users <
[hidden email]>; Patel, Miten <[hidden email]>
Subject: RE: [slicer-users] Making 3D .stl model from DICOM files

 

Hi,

 

According to the dashboard [1], VMTK is available for Mac and Windows (but on Linux there is a persistent build failure apparently). If you install this nightly, then it should be available in extension manager

Windows: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-03-29-win-amd64.exe&checksum=dbcdf1a2ccc8d4298941a31f465faef7

MacOS: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-03-29-macosx-amd64.dmg&checksum=d9176594da4615699f6d36b845b071c6

 

If it’s not in extension manager somehow, then you can install it using the wrench icon in the top left corner of extension manager by choosing this package:

Windows: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=25892-win-amd64-SlicerExtension-VMTK-gite056805-2016-10-21.zip&checksum=24d94af9711ca9280593a8632e65ab56

Mac: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=25892-macosx-amd64-SlicerExtension-VMTK-gite056805-2016-10-21.tar.gz&checksum=333453dca8a67ee281136dd712ec899e

 

Of course if you’re confident in your custom builds, then this will not improve anything, but in case you suspect problems there, it might.

 

csaba

 

[1] http://slicer.cdash.org/index.php?project=Slicer4&filtercount=1&showfilters=1&field1=label&compare1=63&value1=VMTK

 

From: slicer-users [[hidden email]] On Behalf Of Viraj Belekar
Sent: Thursday, March 30, 2017 07:51
To: Andras Lasso <
[hidden email]>
Cc: SPL Slicer Users <
[hidden email]>; Patel, Miten <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello,

 

1) Again, I had downloaded the Nightly Build version and VMTK is not available through the extension manager for it. Please help me in this regard.

 

2) I tried to build Slicer through source code and also compiled VMTK through source code. Is there any tutorial for 'Vesselness filter'? From what I tried to do, the source code version of vmtk is not working. Please help!

 

3) Without using 'Vesselness filter', I tried to extract the vein stl file. But the model is again with fused ends. I want the model to be hollow and without fused(closed) ends. Please help!

 

Thank you very much.

 

Best Regards

Viraj

 

On Thu, Mar 30, 2017 at 11:20 AM, Viraj Belekar <[hidden email]> wrote:

Hi Mr. Andras,

 

I had downloaded the Nightly Build version and VMTK is not available through the extension manager for it.

 

On Wed, Mar 29, 2017 at 6:24 PM, Andras Lasso <[hidden email]> wrote:

VMTK is available now through the extension manager. There is no need to manually download or build anything.

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 29, 2017 3:32


To: Andras Lasso <[hidden email]>
Cc: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello,

 

How do I install VMTK extension as mentioned in the link provided by you? I am following steps on the mentioned here: https://www.slicer.org/wiki/Slicer4:VMTK#Installation

 

But I need a password to use this command: git clone https://haehn@.../haehn/VMTK-in-3D-Slicer.git

 

Thanks

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 5:39 PM, Andras Lasso <[hidden email]> wrote:

To create hollow vessel models, use margin and logical operator effects as described here:

http://slicer-users.65878.n3.nabble.com/Hollow-model-tp4031241p4031242.html

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 28, 2017 7:45
To: Andras Lasso <
[hidden email]>
Cc: Patel, Miten <
[hidden email]>; SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Yes the model should be hollow like a tube as I want to analyse internal flow. If you see the stl file, the ends of the vein are fused which I don't want.

 

 

On Tue, 28 Mar 2017 at 5:10 PM, Andras Lasso <[hidden email]> wrote:

Would you like to make the model hollow (like a tube)?

 

Andras

 

From: [hidden email]
Sent: Tuesday, March 28, 2017 2:12 AM
To: [hidden email]
Cc: [hidden email]; [hidden email]


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

Hello Mr. Andras,

 

By using the technique described by you. I am able to extract a few blood vessel models. The thing is I need to do blood flow analysis using these models. For that I want the end of these veins to be open so that I can define a different surface on these open ends as inlet or outlet. Can you please help?

 

PFA: stl file.

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 10:19 AM, Andras Lasso <[hidden email]> wrote:

> Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Usually you cannot segment vessels by simple thresholding. It’s normal that opacified vessels have the same intensity as bones or other tissues.

 

You can segment the vessel manually: Find a reasonably good threshold range using the threshold effect and click “Use for masking” instead of “Apply”. Then use the paint tool, select “Sphere brush” option, and follow and paint the vessels.

 

You can also try vessel enhancement filter in VMTK extension to enhance vessels and suppress other structures. The vesselness-filtered image will mostly just contain vasculature, so you can extract the vessel tree in the segment editor automatically, by simple thresholding.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Viraj Belekar
Sent: March 28, 2017 0:32
To: Patel, Miten <
[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hi Miten,

 

Can you help me in identifying the threshold range for portal veins? Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Thanks a lot!

 

Regards

Viraj Belekar

 

On Tue, Mar 21, 2017 at 5:29 PM, Patel, Miten <[hidden email]> wrote:

Hi Viraj,

 

Following link and attached tutorial referenced on the web page show the steps to generate an STL from DICOM files.

 

 

The tutorial uses the nightly build rather than 4.6 released version. I've tried it with nightly build from around 15 Mar and it worked fine.

 

The tutorial has extra bits of adding a model etc which you can ignore.

 

We are due to perform the same task for carotid arteries ie STL generation and also centreline extraction for creating geometry for finite element analysis.

 

Would appreciate liaising with you on these steps as looks like we are working on similar tasks.

 

Miten



-------- Original message --------
From: Viraj Belekar <[hidden email]>
Date: 21/03/2017 11:24 (GMT+00:00)
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Making 3D .stl model from DICOM files

Hello everyone,

 

Is there a proper tutorial which addresses making 3D models in .stl format from DICOM files? I want to make a 3D model of portal vein system from DICOM files. Also what should be the threshold range for veins?

 

Thanks and Regards

Viraj Belekar

 

 

 

 


_______________________________________________
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

 

 

 


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Making 3D .stl model from DICOM files

Andras Lasso-2
In reply to this post by Viraj Belekar

How to make thin vessel walls: Resample the input volume to have at least 2-3x smaller voxel size as the thickness of the shell (margin size that you use for growing the shell). At the same time, it is also recommended to crop the volume to the region of interest to keep the volume size reasonable. Crop volume module can do both the resampling and cropping in one combined step. Use the cropped volume as master volume in Segment edditor.

 

Andras

 

From: Csaba Pinter
Sent: April 3, 2017 14:09
To: Viraj Belekar <[hidden email]>; Andras Lasso <[hidden email]>; Slicer Users Mailing List ([hidden email]) <[hidden email]>
Subject: RE: [slicer-users] Making 3D .stl model from DICOM files

 

Hi Viraj,

 

Thanks for the video!

 

The main problem is that you select one segment (green), but want to use the scissors and then the eraser on the other one (yellow), see image

https://www.dropbox.com/s/hbg8ill1feb7f40/20170403_ScissorsIssue.png?dl=0

The selected effect always edits the segment that is selected, and as you select another segment, the operation of course doesn’t work.

 

Also:

- The margin for growing is too small, so the wall of the vessel will not be solid

- You don’t actually cut the end of the vessel wall, but the dilated vessel segmentation
(you probably know the above two, but you did decide to include these steps in the video, so I thought I’d mention)

- I’d use the 2D view to use the scissors, to make sure that there are actual voxels involved. If you do it in the 3D view, you may try to cut a quarter voxel, because you don’t see the underlying “master” representation, which is the labelmap. The surface in the 3D view is mostly for navigation and high-level scissor operations, not precision ones like this one

 

csaba

 

From: Viraj Belekar [[hidden email]]
Sent: Monday, April 3, 2017 13:45
To: Andras Lasso <[hidden email]>; Csaba Pinter <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

​Hello Sirs,

 

Please find the attached file!

 

On Mon, Apr 3, 2017 at 7:18 PM, Andras Lasso <[hidden email]> wrote:

> The scissors tool isntworking with the hollow surface which I create.

 

Please send a screencast (a video that shows what steps you do; not a single screenshot) of your entire segmentation and Slicer application log (menu: Help / Report a bug).

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: April 3, 2017 9:35
To: Andras Lasso <[hidden email]>; Csaba Pinter <[hidden email]>

Cc: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

1) I will send you the screenshot today itself.

 

 

2) The scissors tool isnt working with the hollow surface which I create.

 

 

On Mon, 3 Apr 2017 at 6:55 PM, Csaba Pinter <[hidden email]> wrote:

1) Are you absolutely sure that you have a ‘segmentation’ node and not another type? You can only use Segment Editor with segmentations. Can you go to subject hierarchy and make a screenshot for us to see what you have?

2) You can use the Scissors tool (or simply the Eraser) in Segment Editor to cut off the cap

 

csaba

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: Monday, April 3, 2017 03:24
To: Andras Lasso <
[hidden email]>
Cc: Csaba Pinter <
[hidden email]>; SPL Slicer Users <[hidden email]>; Patel, Miten <[hidden email]>


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello everyone,

 

1) I don't know why vesselness filter isn't working for the LINUX version. When I select a Fiducial using mouse, similar intensity regions get highlighted but when I follow the later steps using Segment Editor and click on 'Create Surface', a surface which includes in the Fiducial point is created and nothing else.

 

2) URGENT! I created a hollow surface of blood vessel by following the steps on this link. I think I did it correctly this time(PFA: stl file). The problem which I want to resolve is that the hollow surface contains fused ends. I need a model with open ends to apply appropriate boundary conditions. Can anyone help in this regard?

 

Thanks and Regards

Viraj Belekar

 

On Thu, Mar 30, 2017 at 7:15 PM, Andras Lasso <[hidden email]> wrote:

The VMTK build error was the usual problem of not setting the C compiler in the external project. I’ve pushed a fix, VMTK extension should appear for linux tomorrow.

 

Andras

 

From: Csaba Pinter
Sent: March 30, 2017 8:54
To: Viraj Belekar <
[hidden email]>; Andras Lasso <[hidden email]>
Cc: SPL Slicer Users <
[hidden email]>; Patel, Miten <[hidden email]>
Subject: RE: [slicer-users] Making 3D .stl model from DICOM files

 

Hi,

 

According to the dashboard [1], VMTK is available for Mac and Windows (but on Linux there is a persistent build failure apparently). If you install this nightly, then it should be available in extension manager

Windows: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-03-29-win-amd64.exe&checksum=dbcdf1a2ccc8d4298941a31f465faef7

MacOS: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-03-29-macosx-amd64.dmg&checksum=d9176594da4615699f6d36b845b071c6

 

If it’s not in extension manager somehow, then you can install it using the wrench icon in the top left corner of extension manager by choosing this package:

Windows: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=25892-win-amd64-SlicerExtension-VMTK-gite056805-2016-10-21.zip&checksum=24d94af9711ca9280593a8632e65ab56

Mac: http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=25892-macosx-amd64-SlicerExtension-VMTK-gite056805-2016-10-21.tar.gz&checksum=333453dca8a67ee281136dd712ec899e

 

Of course if you’re confident in your custom builds, then this will not improve anything, but in case you suspect problems there, it might.

 

csaba

 

[1] http://slicer.cdash.org/index.php?project=Slicer4&filtercount=1&showfilters=1&field1=label&compare1=63&value1=VMTK

 

From: slicer-users [[hidden email]] On Behalf Of Viraj Belekar
Sent: Thursday, March 30, 2017 07:51
To: Andras Lasso <
[hidden email]>
Cc: SPL Slicer Users <
[hidden email]>; Patel, Miten <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello,

 

1) Again, I had downloaded the Nightly Build version and VMTK is not available through the extension manager for it. Please help me in this regard.

 

2) I tried to build Slicer through source code and also compiled VMTK through source code. Is there any tutorial for 'Vesselness filter'? From what I tried to do, the source code version of vmtk is not working. Please help!

 

3) Without using 'Vesselness filter', I tried to extract the vein stl file. But the model is again with fused ends. I want the model to be hollow and without fused(closed) ends. Please help!

 

Thank you very much.

 

Best Regards

Viraj

 

On Thu, Mar 30, 2017 at 11:20 AM, Viraj Belekar <[hidden email]> wrote:

Hi Mr. Andras,

 

I had downloaded the Nightly Build version and VMTK is not available through the extension manager for it.

 

On Wed, Mar 29, 2017 at 6:24 PM, Andras Lasso <[hidden email]> wrote:

VMTK is available now through the extension manager. There is no need to manually download or build anything.

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 29, 2017 3:32


To: Andras Lasso <[hidden email]>
Cc: Patel, Miten <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hello,

 

How do I install VMTK extension as mentioned in the link provided by you? I am following steps on the mentioned here: https://www.slicer.org/wiki/Slicer4:VMTK#Installation

 

But I need a password to use this command: git clone https://haehn@.../haehn/VMTK-in-3D-Slicer.git

 

Thanks

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 5:39 PM, Andras Lasso <[hidden email]> wrote:

To create hollow vessel models, use margin and logical operator effects as described here:

http://slicer-users.65878.n3.nabble.com/Hollow-model-tp4031241p4031242.html

 

Andras

 

From: Viraj Belekar [mailto:[hidden email]]
Sent: March 28, 2017 7:45
To: Andras Lasso <
[hidden email]>
Cc: Patel, Miten <
[hidden email]>; SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Yes the model should be hollow like a tube as I want to analyse internal flow. If you see the stl file, the ends of the vein are fused which I don't want.

 

 

On Tue, 28 Mar 2017 at 5:10 PM, Andras Lasso <[hidden email]> wrote:

Would you like to make the model hollow (like a tube)?

 

Andras

 

From: [hidden email]
Sent: Tuesday, March 28, 2017 2:12 AM
To: [hidden email]
Cc: [hidden email]; [hidden email]


Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

Hello Mr. Andras,

 

By using the technique described by you. I am able to extract a few blood vessel models. The thing is I need to do blood flow analysis using these models. For that I want the end of these veins to be open so that I can define a different surface on these open ends as inlet or outlet. Can you please help?

 

PFA: stl file.

 

Regards

Viraj

 

On Tue, Mar 28, 2017 at 10:19 AM, Andras Lasso <[hidden email]> wrote:

> Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Usually you cannot segment vessels by simple thresholding. It’s normal that opacified vessels have the same intensity as bones or other tissues.

 

You can segment the vessel manually: Find a reasonably good threshold range using the threshold effect and click “Use for masking” instead of “Apply”. Then use the paint tool, select “Sphere brush” option, and follow and paint the vessels.

 

You can also try vessel enhancement filter in VMTK extension to enhance vessels and suppress other structures. The vesselness-filtered image will mostly just contain vasculature, so you can extract the vessel tree in the segment editor automatically, by simple thresholding.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Viraj Belekar
Sent: March 28, 2017 0:32
To: Patel, Miten <
[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Making 3D .stl model from DICOM files

 

Hi Miten,

 

Can you help me in identifying the threshold range for portal veins? Apparently a lot of extra stuff is attached with the veins in the final 3D model.

 

Thanks a lot!

 

Regards

Viraj Belekar

 

On Tue, Mar 21, 2017 at 5:29 PM, Patel, Miten <[hidden email]> wrote:

Hi Viraj,

 

Following link and attached tutorial referenced on the web page show the steps to generate an STL from DICOM files.

 

 

The tutorial uses the nightly build rather than 4.6 released version. I've tried it with nightly build from around 15 Mar and it worked fine.

 

The tutorial has extra bits of adding a model etc which you can ignore.

 

We are due to perform the same task for carotid arteries ie STL generation and also centreline extraction for creating geometry for finite element analysis.

 

Would appreciate liaising with you on these steps as looks like we are working on similar tasks.

 

Miten



-------- Original message --------
From: Viraj Belekar <[hidden email]>
Date: 21/03/2017 11:24 (GMT+00:00)
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Making 3D .stl model from DICOM files

Hello everyone,

 

Is there a proper tutorial which addresses making 3D models in .stl format from DICOM files? I want to make a 3D model of portal vein system from DICOM files. Also what should be the threshold range for veins?

 

Thanks and Regards

Viraj Belekar

 

 

 

 


_______________________________________________
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

 

 

 


_______________________________________________
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