Volume resection

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Volume resection

Rwirz
Hello,
I have running my 3D Slicer with slicerIGT and a tracker system (NDI Polaris). So, I can see in 3D where my probe is. Also, I have a skull segmented with a tumor and I have the 3D volumes of both.
I would like to move the probe in 3D and, when the probe tip touches the volume tumor, erase the portion of the tumor volume that is touching. So, Do you have some idea?
Thank you
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Re: Volume Resection

Tamas Ungi-2
Hi Raul,

I think you need a little programming for this. I would model the tumor using a label volume (not surface model), so you can edit the voxels that come close to your probe tip. You can use the AutoRun button on Model Maker modules to keep a surface model updated every time your label map is modified. So your visualization can be all surface models.

You can probably use a scripted module for proof of concept. Although accessing voxels from python is a bit slow.
Also, be careful with the Model Maker module. There are a couple of unfixed bugs in it. So whenever I can, I use the Grayscale Model Maker instead. Since your tumor is just one label, you can use the Grayscale M M too.

Hope this helps,
Tamas


-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Raul Wirz Gonzalez
Sent: Thursday, November 13, 2014 10:15 AM
To: [hidden email]
Subject: [slicer-users] Volume Resection

Hello,

I have running my 3D Slicer with slicerIGT and a tracker system (NDI Polaris). So, I can see in 3D where my probe is. Also, I have a skull segmented with a tumor and I have the 3D volumes of both.

I would like to move the probe in 3D and, when the probe tip touches the volume tumor, erase the portion of the tumor volume that is touching. So, Do you have some idea?

Thank you
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Working with many models in the Models Module

James Cook
Hello All,
  I've been working with the Models module and have found it to be very inconvenient.
I have a label dataset my lab has been working on. We have 245 labels delineated so far. I've generated models of these labels using the model maker.
  I'm trying to re-arrange these models into a reasonable hierarchy representing the brain ontology.

The following problems exist in the latest release and in the latest nightly.

Selecting multiple models and moving them by dragging them to another model hierarchy node in the models panel doesnt work. Only the clicked model will move into the hierarchy. All the others appear to be in the model hierarchy display, however as soon as you interact with them they revert to their original place.

Once i've dragged a them one at a time into their place they dont like to be re-orderd and I cant see any way to re-order the models based on their name.

Can anyone help point me to a work around for these?

Is there any way to give my colortable the ontological structure so that the model maker will generate the whole hierarchy for me?

I've looked at the subject hierarchy and tried to use the generate structure from disk lay out feature. Unfortunately, the models dont have color information stored with the models so they lose their color when loaded that way. Also the subject hierarchy isnt translated into the model hierarchy and I like the model controls in the models module.

James Cook
CIVM, DUHS
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: Working with many models in the Models Module

Aucoin, Nicole
Hi James,

There is an experimental feature in the Model Maker module, under the
Debug panel, that will allow you to specify a model hierarchy MRML file
to order the output models.  Here's the parameter help text (also
available on the wiki at
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/ModelMaker 
):

A mrml file that contains a template model hierarchy tree with a
hierarchy node per color used in the input volume's color table. Color
names used for the models are matched to template hierarchy names to
create a multi level output tree. Create a hierarchy in the Models GUI
and save a scene, then clean it up to remove everything but the model
hierarchy and display nodes.

It takes a little while to craft the hierarchy, but then it can be
reused every time you run the model maker. The main thing to ensure is
that the names of the hierarchy nodes match the color names in your
table. You'll need to add color table entries for any groups that are
missing.

Let me know if you need more guidance on how to use this feature. I
added it for a local user and it hasn't been extensively tested.

Nicole

On 11/13/14 5:15 PM, James Cook wrote:

> Hello All,
>    I've been working with the Models module and have found it to be very inconvenient.
> I have a label dataset my lab has been working on. We have 245 labels delineated so far. I've generated models of these labels using the model maker.
>    I'm trying to re-arrange these models into a reasonable hierarchy representing the brain ontology.
>
> The following problems exist in the latest release and in the latest nightly.
>
> Selecting multiple models and moving them by dragging them to another model hierarchy node in the models panel doesnt work. Only the clicked model will move into the hierarchy. All the others appear to be in the model hierarchy display, however as soon as you interact with them they revert to their original place.
>
> Once i've dragged a them one at a time into their place they dont like to be re-orderd and I cant see any way to re-order the models based on their name.
>
> Can anyone help point me to a work around for these?
>
> Is there any way to give my colortable the ontological structure so that the model maker will generate the whole hierarchy for me?
>
> I've looked at the subject hierarchy and tried to use the generate structure from disk lay out feature. Unfortunately, the models dont have color information stored with the models so they lose their color when loaded that way. Also the subject hierarchy isnt translated into the model hierarchy and I like the model controls in the models module.
>
> James Cook
> CIVM, DUHS
> _______________________________________________
> 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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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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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: Volume Resection

Andras Lasso-2
In reply to this post by Tamas Ungi-2
Hi Raul,

Based on our experience, volume painting with a tracked tool does not work very well, because even if you use a very thick “brush”, it takes lots of hand-waving is needed to fill a region in 3D.

I would suggest to collect points and clip the volume by the complex hull of the points. You can easily implement this by combining these two simple scripted modules:

1. Build point collection from live tracker input - available in the PositionErrorMapping module


2. Surface model generation from convex hull of points and clip volume - available in Volume clip with surface module


Andras

From: [hidden email]
Sent: ‎Thursday‎, ‎November‎ ‎13‎, ‎2014 ‎1‎:‎33‎ ‎PM
To: [hidden email], [hidden email]

Hi Raul,

I think you need a little programming for this. I would model the tumor using a label volume (not surface model), so you can edit the voxels that come close to your probe tip. You can use the AutoRun button on Model Maker modules to keep a surface model updated every time your label map is modified. So your visualization can be all surface models.

You can probably use a scripted module for proof of concept. Although accessing voxels from python is a bit slow.
Also, be careful with the Model Maker module. There are a couple of unfixed bugs in it. So whenever I can, I use the Grayscale Model Maker instead. Since your tumor is just one label, you can use the Grayscale M M too.

Hope this helps,
Tamas


-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Raul Wirz Gonzalez
Sent: Thursday, November 13, 2014 10:15 AM
To: [hidden email]
Subject: [slicer-users] Volume Resection

Hello,

I have running my 3D Slicer with slicerIGT and a tracker system (NDI Polaris). So, I can see in 3D where my probe is. Also, I have a skull segmented with a tumor and I have the 3D volumes of both.

I would like to move the probe in 3D and, when the probe tip touches the volume tumor, erase the portion of the tumor volume that is touching. So, Do you have some idea?

Thank you
_______________________________________________
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.

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

_______________________________________________
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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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
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Re: Volume Resection

Tamas Ungi-2

I apologize for the incorrect information I gave on Model Maker. All important bugs have been fixed, and it now works with the AutoRun function.

Thanks, Nicole, for pointing this out!

 

Tamas

 

 

From: Andras Lasso
Sent: November 13, 2014 6:26 PM
To: Tamas Ungi; Raul Wirz Gonzalez; [hidden email]
Subject: Re: [slicer-users] Volume Resection

 

Hi Raul,

 

Based on our experience, volume painting with a tracked tool does not work very well, because even if you use a very thick “brush”, it takes lots of hand-waving is needed to fill a region in 3D.

 

I would suggest to collect points and clip the volume by the complex hull of the points. You can easily implement this by combining these two simple scripted modules:

 

1. Build point collection from live tracker input - available in the PositionErrorMapping module

 

 

2. Surface model generation from convex hull of points and clip volume - available in Volume clip with surface module

 

 

Andras

 

From: [hidden email]
Sent: ‎Thursday‎, ‎November‎ ‎13‎, ‎2014 ‎1‎:‎33‎ ‎PM
To: [hidden email], [hidden email]

 

Hi Raul,

I think you need a little programming for this. I would model the tumor using a label volume (not surface model), so you can edit the voxels that come close to your probe tip. You can use the AutoRun button on Model Maker modules to keep a surface model updated every time your label map is modified. So your visualization can be all surface models.

You can probably use a scripted module for proof of concept. Although accessing voxels from python is a bit slow.
Also, be careful with the Model Maker module. There are a couple of unfixed bugs in it. So whenever I can, I use the Grayscale Model Maker instead. Since your tumor is just one label, you can use the Grayscale M M too.

Hope this helps,
Tamas


-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Raul Wirz Gonzalez
Sent: Thursday, November 13, 2014 10:15 AM
To: [hidden email]
Subject: [slicer-users] Volume Resection

Hello,

I have running my 3D Slicer with slicerIGT and a tracker system (NDI Polaris). So, I can see in 3D where my probe is. Also, I have a skull segmented with a tumor and I have the 3D volumes of both.

I would like to move the probe in 3D and, when the probe tip touches the volume tumor, erase the portion of the tumor volume that is touching. So, Do you have some idea?

Thank you
_______________________________________________
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.

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


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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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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
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Re: Working with many models in the Models Module

James Cook
In reply to this post by Aucoin, Nicole
Thank you Nicole.

We have defined the structure now so this should work while we regenerate, however, I'm not successful yet. I've edited a copy of the mrml with the hierarchy leaving only the modelheirarchy nodes, and the model display nodes and model nodes.

Do you happen to have an mrml and color table kicking around to serve as an example?


James Cook
CIVM, DUHS
Work: (919) 684-7672
Cell: (919) 768-3293

________________________________________
From: [hidden email] <[hidden email]> on behalf of Nicole Aucoin <[hidden email]>
Sent: Thursday, November 13, 2014 5:43 PM
To: James Cook; [hidden email]
Subject: Re: [slicer-users] Working with many models in the Models Module

Hi James,

There is an experimental feature in the Model Maker module, under the
Debug panel, that will allow you to specify a model hierarchy MRML file
to order the output models.  Here's the parameter help text (also
available on the wiki at
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/ModelMaker
):

A mrml file that contains a template model hierarchy tree with a
hierarchy node per color used in the input volume's color table. Color
names used for the models are matched to template hierarchy names to
create a multi level output tree. Create a hierarchy in the Models GUI
and save a scene, then clean it up to remove everything but the model
hierarchy and display nodes.

It takes a little while to craft the hierarchy, but then it can be
reused every time you run the model maker. The main thing to ensure is
that the names of the hierarchy nodes match the color names in your
table. You'll need to add color table entries for any groups that are
missing.

Let me know if you need more guidance on how to use this feature. I
added it for a local user and it hasn't been extensively tested.

Nicole

On 11/13/14 5:15 PM, James Cook wrote:

> Hello All,
>    I've been working with the Models module and have found it to be very inconvenient.
> I have a label dataset my lab has been working on. We have 245 labels delineated so far. I've generated models of these labels using the model maker.
>    I'm trying to re-arrange these models into a reasonable hierarchy representing the brain ontology.
>
> The following problems exist in the latest release and in the latest nightly.
>
> Selecting multiple models and moving them by dragging them to another model hierarchy node in the models panel doesnt work. Only the clicked model will move into the hierarchy. All the others appear to be in the model hierarchy display, however as soon as you interact with them they revert to their original place.
>
> Once i've dragged a them one at a time into their place they dont like to be re-orderd and I cant see any way to re-order the models based on their name.
>
> Can anyone help point me to a work around for these?
>
> Is there any way to give my colortable the ontological structure so that the model maker will generate the whole hierarchy for me?
>
> I've looked at the subject hierarchy and tried to use the generate structure from disk lay out feature. Unfortunately, the models dont have color information stored with the models so they lose their color when loaded that way. Also the subject hierarchy isnt translated into the model hierarchy and I like the model controls in the models module.
>
> James Cook
> CIVM, DUHS
> _______________________________________________
> 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.

_______________________________________________
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: Working with many models in the Models Module

Aucoin, Nicole
Hi James,

You need to remove the model nodes and their display nodes, leaving just
the hierarchy nodes and their display nodes.

Here's the project week page from when I was working on this:
http://wiki.na-mic.org/Wiki/index.php/2013_Project_Week:ColorHierarchies
At the top of the Progress section are some example files.
At the bottom there's a link to a script that you can use if you want to
start from a modified color table file to create the template mrml file.

Nicole

On 11/14/14 5:04 PM, James Cook wrote:

> Thank you Nicole.
>
> We have defined the structure now so this should work while we regenerate, however, I'm not successful yet. I've edited a copy of the mrml with the hierarchy leaving only the modelheirarchy nodes, and the model display nodes and model nodes.
>
> Do you happen to have an mrml and color table kicking around to serve as an example?
>
>
> James Cook
> CIVM, DUHS
> Work: (919) 684-7672
> Cell: (919) 768-3293
>
> ________________________________________
> From: [hidden email] <[hidden email]> on behalf of Nicole Aucoin <[hidden email]>
> Sent: Thursday, November 13, 2014 5:43 PM
> To: James Cook; [hidden email]
> Subject: Re: [slicer-users] Working with many models in the Models Module
>
> Hi James,
>
> There is an experimental feature in the Model Maker module, under the
> Debug panel, that will allow you to specify a model hierarchy MRML file
> to order the output models.  Here's the parameter help text (also
> available on the wiki at
> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/ModelMaker
> ):
>
> A mrml file that contains a template model hierarchy tree with a
> hierarchy node per color used in the input volume's color table. Color
> names used for the models are matched to template hierarchy names to
> create a multi level output tree. Create a hierarchy in the Models GUI
> and save a scene, then clean it up to remove everything but the model
> hierarchy and display nodes.
>
> It takes a little while to craft the hierarchy, but then it can be
> reused every time you run the model maker. The main thing to ensure is
> that the names of the hierarchy nodes match the color names in your
> table. You'll need to add color table entries for any groups that are
> missing.
>
> Let me know if you need more guidance on how to use this feature. I
> added it for a local user and it hasn't been extensively tested.
>
> Nicole
>
> On 11/13/14 5:15 PM, James Cook wrote:
>> Hello All,
>>     I've been working with the Models module and have found it to be very inconvenient.
>> I have a label dataset my lab has been working on. We have 245 labels delineated so far. I've generated models of these labels using the model maker.
>>     I'm trying to re-arrange these models into a reasonable hierarchy representing the brain ontology.
>>
>> The following problems exist in the latest release and in the latest nightly.
>>
>> Selecting multiple models and moving them by dragging them to another model hierarchy node in the models panel doesnt work. Only the clicked model will move into the hierarchy. All the others appear to be in the model hierarchy display, however as soon as you interact with them they revert to their original place.
>>
>> Once i've dragged a them one at a time into their place they dont like to be re-orderd and I cant see any way to re-order the models based on their name.
>>
>> Can anyone help point me to a work around for these?
>>
>> Is there any way to give my colortable the ontological structure so that the model maker will generate the whole hierarchy for me?
>>
>> I've looked at the subject hierarchy and tried to use the generate structure from disk lay out feature. Unfortunately, the models dont have color information stored with the models so they lose their color when loaded that way. Also the subject hierarchy isnt translated into the model hierarchy and I like the model controls in the models module.
>>
>> James Cook
>> CIVM, DUHS
>> _______________________________________________
>> 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.
>

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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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