building a solid mesh

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building a solid mesh

Murat Maga

Hi,

 

I need to build  solid meshes that has no interior from CT scans (no endocranial space, no nasal and maxillary sinuses etc). Since there are quite a few, I want to find a quick or scriptable way of doing this. Currently I go into Editor module and plug in every space. While it gets the job done, it takes time.

 

Are there any modules/extensions that may help me cut down the processing time?

 

Best,

Murat


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Re: building a solid mesh

Kikinis, Ron,M.D.
Hi Murat,

Nice monkey skull.

Have you looked at the "remove islands" effect in the editor? That one works in 3D and should be fast. If there are leaks in 3D, you can plug them in the slices. The "identify islands" effect will allow you to see what is connected to what in 3D.

Best

Ron


On Jun 5, 2016, at 7:11 PM, Murat Maga <[hidden email]> wrote:

Hi,
 
I need to build  solid meshes that has no interior from CT scans (no endocranial space, no nasal and maxillary sinuses etc). Since there are quite a few, I want to find a quick or scriptable way of doing this. Currently I go into Editor module and plug in every space. While it gets the job done, it takes time. 
 
Are there any modules/extensions that may help me cut down the processing time?
 
Best,
Murat
<Capture.png>_______________________________________________
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[hidden email]
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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-- 
Ron Kikinis, M.D.,
Robert Greenes Distinguished Director of Biomedical Informatics
Professor of Radiology, Harvard Medical School
Director, Surgical Planning Laboratory
http://www.spl.harvard.edu/~kikinis


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Re: building a solid mesh

Murat Maga
In reply to this post by Murat Maga

Hi Ron,

 

Yeah, I use the island effect to remove the foam padding skulls were placed to during the scan. It is really the next step of plugging all holes for cranial foramina and the endocranial space is taking really long to do manually. The way I currently do, I need to go into the editor use a combination of magic wand and paint to fill all the spaces. It is doable for a few skulls but not for dozens…

 

Best,

M

 

 

 

From: Kikinis, Ron,M.D. [mailto:[hidden email]]
Sent: Tuesday, June 07, 2016 12:59 AM
To: Murat Maga
Cc: SPL Slicer Users
Subject: Re: [slicer-users] building a solid mesh

 

Hi Murat,

 

Nice monkey skull.

 

Have you looked at the "remove islands" effect in the editor? That one works in 3D and should be fast. If there are leaks in 3D, you can plug them in the slices. The "identify islands" effect will allow you to see what is connected to what in 3D.

 

Best

 

Ron

 

 

On Jun 5, 2016, at 7:11 PM, Murat Maga <[hidden email]> wrote:

 

Hi,

 

I need to build  solid meshes that has no interior from CT scans (no endocranial space, no nasal and maxillary sinuses etc). Since there are quite a few, I want to find a quick or scriptable way of doing this. Currently I go into Editor module and plug in every space. While it gets the job done, it takes time. 

 

Are there any modules/extensions that may help me cut down the processing time?

 

Best,

Murat

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

 

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

 

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


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Re: building a solid mesh

Andras Lasso-2

You may also try the new Segment editor in SlicerRT (latest nightly version). The Smoothing effect has a Closing method that fills cavities up to a specified size.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Murat Maga
Sent: June 7, 2016 1:58 PM
To: Kikinis, Ron,M.D. <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] building a solid mesh

 

Hi Ron,

 

Yeah, I use the island effect to remove the foam padding skulls were placed to during the scan. It is really the next step of plugging all holes for cranial foramina and the endocranial space is taking really long to do manually. The way I currently do, I need to go into the editor use a combination of magic wand and paint to fill all the spaces. It is doable for a few skulls but not for dozens…

 

Best,

M

 

 

 

From: Kikinis, Ron,M.D. [[hidden email]]
Sent: Tuesday, June 07, 2016 12:59 AM
To: Murat Maga
Cc: SPL Slicer Users
Subject: Re: [slicer-users] building a solid mesh

 

Hi Murat,

 

Nice monkey skull.

 

Have you looked at the "remove islands" effect in the editor? That one works in 3D and should be fast. If there are leaks in 3D, you can plug them in the slices. The "identify islands" effect will allow you to see what is connected to what in 3D.

 

Best

 

Ron

 

 

On Jun 5, 2016, at 7:11 PM, Murat Maga <[hidden email]> wrote:

 

Hi,

 

I need to build  solid meshes that has no interior from CT scans (no endocranial space, no nasal and maxillary sinuses etc). Since there are quite a few, I want to find a quick or scriptable way of doing this. Currently I go into Editor module and plug in every space. While it gets the job done, it takes time. 

 

Are there any modules/extensions that may help me cut down the processing time?

 

Best,

Murat

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

 

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

 

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


_______________________________________________
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: building a solid mesh

arumiat
What is the end goal you're trying to achieve, it would take 10 minutes in a sculpting program

------------------------------------
V A L A design
+ 4 4 (0) 2 0 3 6 3 7 0 0 6 2
IVALA LTD.   REG NO.7931234


On 9 June 2016 at 03:13, Andras Lasso <[hidden email]> wrote:

You may also try the new Segment editor in SlicerRT (latest nightly version). The Smoothing effect has a Closing method that fills cavities up to a specified size.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Murat Maga
Sent: June 7, 2016 1:58 PM
To: Kikinis, Ron,M.D. <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] building a solid mesh

 

Hi Ron,

 

Yeah, I use the island effect to remove the foam padding skulls were placed to during the scan. It is really the next step of plugging all holes for cranial foramina and the endocranial space is taking really long to do manually. The way I currently do, I need to go into the editor use a combination of magic wand and paint to fill all the spaces. It is doable for a few skulls but not for dozens…

 

Best,

M

 

 

 

From: Kikinis, Ron,M.D. [[hidden email]]
Sent: Tuesday, June 07, 2016 12:59 AM
To: Murat Maga
Cc: SPL Slicer Users
Subject: Re: [slicer-users] building a solid mesh

 

Hi Murat,

 

Nice monkey skull.

 

Have you looked at the "remove islands" effect in the editor? That one works in 3D and should be fast. If there are leaks in 3D, you can plug them in the slices. The "identify islands" effect will allow you to see what is connected to what in 3D.

 

Best

 

Ron

 

 

On Jun 5, 2016, at 7:11 PM, Murat Maga <[hidden email]> wrote:

 

Hi,

 

I need to build  solid meshes that has no interior from CT scans (no endocranial space, no nasal and maxillary sinuses etc). Since there are quite a few, I want to find a quick or scriptable way of doing this. Currently I go into Editor module and plug in every space. While it gets the job done, it takes time. 

 

Are there any modules/extensions that may help me cut down the processing time?

 

Best,

Murat

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

 

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

 

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


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


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Re: building a solid mesh

Murat Maga
In reply to this post by Andras Lasso-2

Hi Taimur,

 

The downstream application is shape analysis. It will happen either through a particle distribution system like Shapeworks (in which case, I will use the label maps) or geometric morphometrics methods where you sample thousands of equally spaced points on the surface of the mesh. In my experience both methods fail, if there are internal cavities, hence the need to fill the void.

 

I am not familiar with sculpting, is through Blender or likes?

Best,

M

 

 

 

From: Taimur Alavi [mailto:[hidden email]]
Sent: Friday, June 10, 2016 2:47 AM
To: Andras Lasso
Cc: Murat Maga; Kikinis, Ron,M.D.; SPL Slicer Users
Subject: Re: [slicer-users] building a solid mesh

 

What is the end goal you're trying to achieve, it would take 10 minutes in a sculpting program


------------------------------------

I V A L A design

+ 4 4 (0) 2 0 3 6 3 7 0 0 6 2

IVALA LTD.   REG NO.7931234

  •  

 

On 9 June 2016 at 03:13, Andras Lasso <[hidden email]> wrote:

You may also try the new Segment editor in SlicerRT (latest nightly version). The Smoothing effect has a Closing method that fills cavities up to a specified size.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Murat Maga
Sent: June 7, 2016 1:58 PM
To: Kikinis, Ron,M.D. <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] building a solid mesh

 

Hi Ron,

 

Yeah, I use the island effect to remove the foam padding skulls were placed to during the scan. It is really the next step of plugging all holes for cranial foramina and the endocranial space is taking really long to do manually. The way I currently do, I need to go into the editor use a combination of magic wand and paint to fill all the spaces. It is doable for a few skulls but not for dozens…

 

Best,

M

 

 

 

From: Kikinis, Ron,M.D. [[hidden email]]
Sent: Tuesday, June 07, 2016 12:59 AM
To: Murat Maga
Cc: SPL Slicer Users
Subject: Re: [slicer-users] building a solid mesh

 

Hi Murat,

 

Nice monkey skull.

 

Have you looked at the "remove islands" effect in the editor? That one works in 3D and should be fast. If there are leaks in 3D, you can plug them in the slices. The "identify islands" effect will allow you to see what is connected to what in 3D.

 

Best

 

Ron

 

 

On Jun 5, 2016, at 7:11 PM, Murat Maga <[hidden email]> wrote:

 

Hi,

 

I need to build  solid meshes that has no interior from CT scans (no endocranial space, no nasal and maxillary sinuses etc). Since there are quite a few, I want to find a quick or scriptable way of doing this. Currently I go into Editor module and plug in every space. While it gets the job done, it takes time. 

 

Are there any modules/extensions that may help me cut down the processing time?

 

Best,

Murat

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

 

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

 

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


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

 


_______________________________________________
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Re: building a solid mesh

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

Have you tried “Closing” operation in the Segment editor module? It should fill all the small holes without changing anything else. If a few big cavities are left then you can fill them using the paint tool (choose a large radius and sphere brush). It shouldn't take more than a couple of minutes.

 

Andras

 

From: [hidden email]
Sent: June 10, 2016 14:28
To: [hidden email]; [hidden email]
Cc: [hidden email]; [hidden email]
Subject: RE: [slicer-users] building a solid mesh

 

Hi Taimur,

 

The downstream application is shape analysis. It will happen either through a particle distribution system like Shapeworks (in which case, I will use the label maps) or geometric morphometrics methods where you sample thousands of equally spaced points on the surface of the mesh. In my experience both methods fail, if there are internal cavities, hence the need to fill the void.

 

I am not familiar with sculpting, is through Blender or likes?

Best,

M

 

 

 

From: Taimur Alavi [mailto:[hidden email]]
Sent: Friday, June 10, 2016 2:47 AM
To: Andras Lasso
Cc: Murat Maga; Kikinis, Ron,M.D.; SPL Slicer Users
Subject: Re: [slicer-users] building a solid mesh

 

What is the end goal you're trying to achieve, it would take 10 minutes in a sculpting program


------------------------------------

I V A L A design

+ 4 4 (0) 2 0 3 6 3 7 0 0 6 2

IVALA LTD.   REG NO.7931234

  •  

 

On 9 June 2016 at 03:13, Andras Lasso <[hidden email]> wrote:

You may also try the new Segment editor in SlicerRT (latest nightly version). The Smoothing effect has a Closing method that fills cavities up to a specified size.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Murat Maga
Sent: June 7, 2016 1:58 PM
To: Kikinis, Ron,M.D. <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] building a solid mesh

 

Hi Ron,

 

Yeah, I use the island effect to remove the foam padding skulls were placed to during the scan. It is really the next step of plugging all holes for cranial foramina and the endocranial space is taking really long to do manually. The way I currently do, I need to go into the editor use a combination of magic wand and paint to fill all the spaces. It is doable for a few skulls but not for dozens…

 

Best,

M

 

 

 

From: Kikinis, Ron,M.D. [[hidden email]]
Sent: Tuesday, June 07, 2016 12:59 AM
To: Murat Maga
Cc: SPL Slicer Users
Subject: Re: [slicer-users] building a solid mesh

 

Hi Murat,

 

Nice monkey skull.

 

Have you looked at the "remove islands" effect in the editor? That one works in 3D and should be fast. If there are leaks in 3D, you can plug them in the slices. The "identify islands" effect will allow you to see what is connected to what in 3D.

 

Best

 

Ron

 

 

On Jun 5, 2016, at 7:11 PM, Murat Maga <[hidden email]> wrote:

 

Hi,

 

I need to build  solid meshes that has no interior from CT scans (no endocranial space, no nasal and maxillary sinuses etc). Since there are quite a few, I want to find a quick or scriptable way of doing this. Currently I go into Editor module and plug in every space. While it gets the job done, it takes time. 

 

Are there any modules/extensions that may help me cut down the processing time?

 

Best,

Murat

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

 

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

 

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


_______________________________________________
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
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Re: building a solid mesh

arumiat
In reply to this post by Andras Lasso-2
Yes, a sculpting software, if you're happy to share your mesh or an example mesh I'll try for you

------------------------------------
V A L A design
+ 4 4 (0) 2 0 3 6 3 7 0 0 6 2
IVALA LTD.   REG NO.7931234


On 11 June 2016 at 05:31, Andras Lasso <[hidden email]> wrote:

Have you tried “Closing” operation in the Segment editor module? It should fill all the small holes without changing anything else. If a few big cavities are left then you can fill them using the paint tool (choose a large radius and sphere brush). It shouldn't take more than a couple of minutes.

 

Andras

 

From: [hidden email]
Sent: June 10, 2016 14:28
To: [hidden email]; [hidden email]
Cc: [hidden email]; [hidden email]
Subject: RE: [slicer-users] building a solid mesh

 

Hi Taimur,

 

The downstream application is shape analysis. It will happen either through a particle distribution system like Shapeworks (in which case, I will use the label maps) or geometric morphometrics methods where you sample thousands of equally spaced points on the surface of the mesh. In my experience both methods fail, if there are internal cavities, hence the need to fill the void.

 

I am not familiar with sculpting, is through Blender or likes?

Best,

M

 

 

 

From: Taimur Alavi [mailto:[hidden email]]
Sent: Friday, June 10, 2016 2:47 AM
To: Andras Lasso
Cc: Murat Maga; Kikinis, Ron,M.D.; SPL Slicer Users
Subject: Re: [slicer-users] building a solid mesh

 

What is the end goal you're trying to achieve, it would take 10 minutes in a sculpting program


------------------------------------

I V A L A design

+ 4 4 (0) 2 0 3 6 3 7 0 0 6 2

IVALA LTD.   REG NO.7931234

  •  

 

On 9 June 2016 at 03:13, Andras Lasso <[hidden email]> wrote:

You may also try the new Segment editor in SlicerRT (latest nightly version). The Smoothing effect has a Closing method that fills cavities up to a specified size.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Murat Maga
Sent: June 7, 2016 1:58 PM
To: Kikinis, Ron,M.D. <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>


Subject: Re: [slicer-users] building a solid mesh

 

Hi Ron,

 

Yeah, I use the island effect to remove the foam padding skulls were placed to during the scan. It is really the next step of plugging all holes for cranial foramina and the endocranial space is taking really long to do manually. The way I currently do, I need to go into the editor use a combination of magic wand and paint to fill all the spaces. It is doable for a few skulls but not for dozens…

 

Best,

M

 

 

 

From: Kikinis, Ron,M.D. [[hidden email]]
Sent: Tuesday, June 07, 2016 12:59 AM
To: Murat Maga
Cc: SPL Slicer Users
Subject: Re: [slicer-users] building a solid mesh

 

Hi Murat,

 

Nice monkey skull.

 

Have you looked at the "remove islands" effect in the editor? That one works in 3D and should be fast. If there are leaks in 3D, you can plug them in the slices. The "identify islands" effect will allow you to see what is connected to what in 3D.

 

Best

 

Ron

 

 

On Jun 5, 2016, at 7:11 PM, Murat Maga <[hidden email]> wrote:

 

Hi,

 

I need to build  solid meshes that has no interior from CT scans (no endocranial space, no nasal and maxillary sinuses etc). Since there are quite a few, I want to find a quick or scriptable way of doing this. Currently I go into Editor module and plug in every space. While it gets the job done, it takes time. 

 

Are there any modules/extensions that may help me cut down the processing time?

 

Best,

Murat

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

 

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

 

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


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

 



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