Reducing mesh size of multi-compartment mesh model

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

Reducing mesh size of multi-compartment mesh model

ttat
I used the model-maker (w/ join smoothing) to generate a multi-compartment
mesh model. However, the mesh size is too big (file size of one compartment
is > 1GB) and therefore I need to significantly reduce the size before I
could import it into a volumetric mesh generator. I read that I should use
surface-toolbox to clean the surface mesh, but it appears I can only clean
one compartment at a time, and I'm afraid that it may alter the surface
geometry (and then the compartments won't fit  each other).... Can anyone
plz give me some suggestions?



--
View this message in context: http://slicer-users.65878.n3.nabble.com/Reducing-mesh-size-of-multi-compartment-mesh-model-tp4030243.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
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


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.

Reply | Threaded
Open this post in threaded view
|

Re: Reducing mesh size of multi-compartment mesh model

Andrey Fedorov-2
I would not say that Slicer is the most powerful tool for cleaning up
surface meshes.

If I were you, I would explore other options using more specialized
packages such as MeshLab http://meshlab.sourceforge.net/

On Wed, Apr 6, 2016 at 11:51 AM, ttat <[hidden email]> wrote:

> I used the model-maker (w/ join smoothing) to generate a multi-compartment
> mesh model. However, the mesh size is too big (file size of one compartment
> is > 1GB) and therefore I need to significantly reduce the size before I
> could import it into a volumetric mesh generator. I read that I should use
> surface-toolbox to clean the surface mesh, but it appears I can only clean
> one compartment at a time, and I'm afraid that it may alter the surface
> geometry (and then the compartments won't fit  each other).... Can anyone
> plz give me some suggestions?
>
>
>
> --
> View this message in context: http://slicer-users.65878.n3.nabble.com/Reducing-mesh-size-of-multi-compartment-mesh-model-tp4030243.html
> Sent from the slicer-users mailing list archive at Nabble.com.
> _______________________________________________
> 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
>
>
> 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
Reply | Threaded
Open this post in threaded view
|

Re: Reducing mesh size of multi-compartment mesh model

Andras Lasso-2
In reply to this post by ttat
The simplest is to reduce the input volume's resolution.

If you don't want to do that then you can play with VTK filters: set compartment ID as cell attribute in each mesh, append all the meshes into one mesh, decimate the combined mesh, and finally (if you need separate mesh for each compartment) split the mesh using cell attribute. This is pure VTK processing, so if you have any questions about this then you may ask further help on the VTK users mailing list.

Andras

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of ttat
Sent: April 6, 2016 11:51 AM
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Reducing mesh size of multi-compartment mesh model

I used the model-maker (w/ join smoothing) to generate a multi-compartment mesh model. However, the mesh size is too big (file size of one compartment is > 1GB) and therefore I need to significantly reduce the size before I could import it into a volumetric mesh generator. I read that I should use surface-toolbox to clean the surface mesh, but it appears I can only clean one compartment at a time, and I'm afraid that it may alter the surface geometry (and then the compartments won't fit  each other).... Can anyone plz give me some suggestions?



--
View this message in context: http://slicer-users.65878.n3.nabble.com/Reducing-mesh-size-of-multi-compartment-mesh-model-tp4030243.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
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


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
Reply | Threaded
Open this post in threaded view
|

Re: Reducing mesh size of multi-compartment mesh model

ttat
In reply to this post by ttat
Dear Andras,

Many thanks for your reply. At this stage I can't reduce the resolution, as some regions are only 1 or 2 pixels thin so if I reduce the resolution they might disappear.

I don't understand your suggestions on VTK filters... Is it a module of Slicer or a different software?

Best,
Will

> On 06 Apr 2016, at 18:08, Andras Lasso <[hidden email]> wrote:
>
> The simplest is to reduce the input volume's resolution.
>
> If you don't want to do that then you can play with VTK filters: set compartment ID as cell attribute in each mesh, append all the meshes into one mesh, decimate the combined mesh, and finally (if you need separate mesh for each compartment) split the mesh using cell attribute. This is pure VTK processing, so if you have any questions about this then you may ask further help on the VTK users mailing list.
>
> Andras
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On Behalf Of ttat
> Sent: April 6, 2016 11:51 AM
> To: SPL Slicer Users <[hidden email]>
> Subject: [slicer-users] Reducing mesh size of multi-compartment mesh model
>
> I used the model-maker (w/ join smoothing) to generate a multi-compartment mesh model. However, the mesh size is too big (file size of one compartment is > 1GB) and therefore I need to significantly reduce the size before I could import it into a volumetric mesh generator. I read that I should use surface-toolbox to clean the surface mesh, but it appears I can only clean one compartment at a time, and I'm afraid that it may alter the surface geometry (and then the compartments won't fit  each other).... Can anyone plz give me some suggestions?
>
>
>
> --
> View this message in context: http://slicer-users.65878.n3.nabble.com/Reducing-mesh-size-of-multi-compartment-mesh-model-tp4030243.html
> Sent from the slicer-users mailing list archive at Nabble.com.
> _______________________________________________
> 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
>
>
> 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
Reply | Threaded
Open this post in threaded view
|

Re: Reducing mesh size of multi-compartment mesh model

Steve Pieper-2
@Andrey - does meshlab handle watertight multicompartment models?  I didn't see that on their web site.

@Will - did you try changing the smoothing and decimation options in the ModelMaker?  Those might be the best option for reducing the model size but it's likely that any smoothing is going to change or remove the small features of your models.

HTH,
Steve

On Wed, Apr 6, 2016 at 3:33 PM, SW.B.Whelan <[hidden email]> wrote:
Dear Andras,

Many thanks for your reply. At this stage I can't reduce the resolution, as some regions are only 1 or 2 pixels thin so if I reduce the resolution they might disappear.

I don't understand your suggestions on VTK filters... Is it a module of Slicer or a different software?

Best,
Will

> On 06 Apr 2016, at 18:08, Andras Lasso <[hidden email]> wrote:
>
> The simplest is to reduce the input volume's resolution.
>
> If you don't want to do that then you can play with VTK filters: set compartment ID as cell attribute in each mesh, append all the meshes into one mesh, decimate the combined mesh, and finally (if you need separate mesh for each compartment) split the mesh using cell attribute. This is pure VTK processing, so if you have any questions about this then you may ask further help on the VTK users mailing list.
>
> Andras
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On Behalf Of ttat
> Sent: April 6, 2016 11:51 AM
> To: SPL Slicer Users <[hidden email]>
> Subject: [slicer-users] Reducing mesh size of multi-compartment mesh model
>
> I used the model-maker (w/ join smoothing) to generate a multi-compartment mesh model. However, the mesh size is too big (file size of one compartment is > 1GB) and therefore I need to significantly reduce the size before I could import it into a volumetric mesh generator. I read that I should use surface-toolbox to clean the surface mesh, but it appears I can only clean one compartment at a time, and I'm afraid that it may alter the surface geometry (and then the compartments won't fit  each other).... Can anyone plz give me some suggestions?
>
>
>
> --
> View this message in context: http://slicer-users.65878.n3.nabble.com/Reducing-mesh-size-of-multi-compartment-mesh-model-tp4030243.html
> Sent from the slicer-users mailing list archive at Nabble.com.
> _______________________________________________
> 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
>
>
> 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
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


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.
Reply | Threaded
Open this post in threaded view
|

Re: Reducing mesh size of multi-compartment mesh model

Andrey Fedorov-2

@Steve - I don't know, all I know it was useful when I worked with surface meshes, and it might worth exploring.

On Apr 6, 2016 19:50, "Steve Pieper" <[hidden email]> wrote:
@Andrey - does meshlab handle watertight multicompartment models?  I didn't see that on their web site.

@Will - did you try changing the smoothing and decimation options in the ModelMaker?  Those might be the best option for reducing the model size but it's likely that any smoothing is going to change or remove the small features of your models.

HTH,
Steve

On Wed, Apr 6, 2016 at 3:33 PM, SW.B.Whelan <[hidden email]> wrote:
Dear Andras,

Many thanks for your reply. At this stage I can't reduce the resolution, as some regions are only 1 or 2 pixels thin so if I reduce the resolution they might disappear.

I don't understand your suggestions on VTK filters... Is it a module of Slicer or a different software?

Best,
Will

> On 06 Apr 2016, at 18:08, Andras Lasso <[hidden email]> wrote:
>
> The simplest is to reduce the input volume's resolution.
>
> If you don't want to do that then you can play with VTK filters: set compartment ID as cell attribute in each mesh, append all the meshes into one mesh, decimate the combined mesh, and finally (if you need separate mesh for each compartment) split the mesh using cell attribute. This is pure VTK processing, so if you have any questions about this then you may ask further help on the VTK users mailing list.
>
> Andras
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On Behalf Of ttat
> Sent: April 6, 2016 11:51 AM
> To: SPL Slicer Users <[hidden email]>
> Subject: [slicer-users] Reducing mesh size of multi-compartment mesh model
>
> I used the model-maker (w/ join smoothing) to generate a multi-compartment mesh model. However, the mesh size is too big (file size of one compartment is > 1GB) and therefore I need to significantly reduce the size before I could import it into a volumetric mesh generator. I read that I should use surface-toolbox to clean the surface mesh, but it appears I can only clean one compartment at a time, and I'm afraid that it may alter the surface geometry (and then the compartments won't fit  each other).... Can anyone plz give me some suggestions?
>
>
>
> --
> View this message in context: http://slicer-users.65878.n3.nabble.com/Reducing-mesh-size-of-multi-compartment-mesh-model-tp4030243.html
> Sent from the slicer-users mailing list archive at Nabble.com.
> _______________________________________________
> 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
>
>
> 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
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


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


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.
Reply | Threaded
Open this post in threaded view
|

Re: Reducing mesh size of multi-compartment mesh model

ttat
In reply to this post by Steve Pieper-2
@Steve: I know... That's why I am hoping there are other tools for me to deal with this problem. If I only increase decimation, will it change the geometry?
@Andras: Can you please tell me where the VTK filters you mentioned are? Is it in meshlab? Can > 2 GB total size be imported in it (it crashed when trying to be imported in Blender).

On 07 Apr 2016, at 02:10, Andrey Fedorov <[hidden email]> wrote:

@Steve - I don't know, all I know it was useful when I worked with surface meshes, and it might worth exploring.

On Apr 6, 2016 19:50, "Steve Pieper" <[hidden email]> wrote:
@Andrey - does meshlab handle watertight multicompartment models?  I didn't see that on their web site.

@Will - did you try changing the smoothing and decimation options in the ModelMaker?  Those might be the best option for reducing the model size but it's likely that any smoothing is going to change or remove the small features of your models.

HTH,
Steve

On Wed, Apr 6, 2016 at 3:33 PM, SW.B.Whelan <[hidden email]> wrote:
Dear Andras,

Many thanks for your reply. At this stage I can't reduce the resolution, as some regions are only 1 or 2 pixels thin so if I reduce the resolution they might disappear.

I don't understand your suggestions on VTK filters... Is it a module of Slicer or a different software?

Best,
Will

> On 06 Apr 2016, at 18:08, Andras Lasso <[hidden email]> wrote:
>
> The simplest is to reduce the input volume's resolution.
>
> If you don't want to do that then you can play with VTK filters: set compartment ID as cell attribute in each mesh, append all the meshes into one mesh, decimate the combined mesh, and finally (if you need separate mesh for each compartment) split the mesh using cell attribute. This is pure VTK processing, so if you have any questions about this then you may ask further help on the VTK users mailing list.
>
> Andras
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On Behalf Of ttat
> Sent: April 6, 2016 11:51 AM
> To: SPL Slicer Users <[hidden email]>
> Subject: [slicer-users] Reducing mesh size of multi-compartment mesh model
>
> I used the model-maker (w/ join smoothing) to generate a multi-compartment mesh model. However, the mesh size is too big (file size of one compartment is > 1GB) and therefore I need to significantly reduce the size before I could import it into a volumetric mesh generator. I read that I should use surface-toolbox to clean the surface mesh, but it appears I can only clean one compartment at a time, and I'm afraid that it may alter the surface geometry (and then the compartments won't fit  each other).... Can anyone plz give me some suggestions?
>
>
>
> --
> View this message in context: http://slicer-users.65878.n3.nabble.com/Reducing-mesh-size-of-multi-compartment-mesh-model-tp4030243.html
> Sent from the slicer-users mailing list archive at Nabble.com.
> _______________________________________________
> 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
>
>
> 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
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


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


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.