Re: 3D model to rtstruct. . .

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Re: 3D model to rtstruct. . .

Sharp, Gregory C.
Hi Dave,

I hope it's ok that I cc your question to the slicer e-mail list,
since your question has quite general interest.

Your goal can be accomplished in 10 easy steps.  ;)

(1a) Load the STL file as a model
(1b) Load your reference CT as a DICOM volume
(2a) Go to the segmentation module.  
(2b) Near the top, at the "Current segmentation" dropdown,
choose "Create new segmentation"
(2c) At the bottom is a widget called "Copy/move segment (import/export)"
In the dropdown, choose your model.
(2d) Click the "<+" button to move the model into the segmentation
(3a) Go to the segmentation module
(3b) Drag your segmentation under the patient study
(3c) Right click on the segmentation, and choose "Export to DICOM..."

NOTE: If you are not using a recent nightly build, the procedure may be different,
or it may not even be possible.  Also, you must install the SlicerRT extension.

Greg


From: David Sasaki [mailto:[hidden email]]
Sent: Tuesday, August 18, 2015 9:58 AM
To: Sharp, Gregory C.
Subject: 3D model to rtstruct. . .

Hi Dr. Sharp,
 
I'm sure you're very busy, so I'll keep it short:
 
Is it possible to take something from STL or PLY to rtstruct in Slicer?  I've been trying for over a day now, and can't seem to get it to work.  Not sure if I'm attempting something that isn't possible, or if I just can't overcome my own ignorance.  I'd like to take a 3D model and try to import it into Eclipse.  Can explain why if that would help.
 
Thanks for any help you can give me.  The Autoseg symposium you gave at the World Congress was very good.
 
Dave.
 
David Sasaki, M. Sc., MCCPM
CancerCare Manitoba
Winnipeg, MB
Canada
This email and/or any documents in this transmission is intended for the
addressee(s) only and may contain legally privileged or confidential information.  Any unauthorized use, disclosure, distribution, copying or dissemination is strictly prohibited.  If you receive this transmission in error, please notify the sender immediately and return the original.
Ce courriel et tout document dans cette transmission est destiné à la personne ou aux personnes à qui il est adressé. Il peut contenir des informations privilégiées ou confidentielles. Toute utilisation, divulgation, distribution, copie, ou diffusion non autorisée est strictement défendue. Si vous n'êtes pas le destinataire de ce message, veuillez en informer l'expéditeur immédiatement et lui remettre l'original.
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Re: 3D model to rtstruct. . .

Sharp, Gregory C.
One correction.

(3a) Go to the Subject Hierarchy module.


-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Sharp, Gregory C.
Sent: Tuesday, August 18, 2015 10:38 AM
To: 'David Sasaki'
Cc: SPL Slicer Users
Subject: Re: [slicer-users] 3D model to rtstruct. . .

Hi Dave,

I hope it's ok that I cc your question to the slicer e-mail list, since your question has quite general interest.

Your goal can be accomplished in 10 easy steps.  ;)

(1a) Load the STL file as a model
(1b) Load your reference CT as a DICOM volume
(2a) Go to the segmentation module.  
(2b) Near the top, at the "Current segmentation" dropdown, choose "Create new segmentation"
(2c) At the bottom is a widget called "Copy/move segment (import/export)"
In the dropdown, choose your model.
(2d) Click the "<+" button to move the model into the segmentation
(3a) Go to the segmentation module
(3b) Drag your segmentation under the patient study
(3c) Right click on the segmentation, and choose "Export to DICOM..."

NOTE: If you are not using a recent nightly build, the procedure may be different, or it may not even be possible.  Also, you must install the SlicerRT extension.

Greg


From: David Sasaki [mailto:[hidden email]]
Sent: Tuesday, August 18, 2015 9:58 AM
To: Sharp, Gregory C.
Subject: 3D model to rtstruct. . .

Hi Dr. Sharp,
 
I'm sure you're very busy, so I'll keep it short:
 
Is it possible to take something from STL or PLY to rtstruct in Slicer?  I've been trying for over a day now, and can't seem to get it to work.  Not sure if I'm attempting something that isn't possible, or if I just can't overcome my own ignorance.  I'd like to take a 3D model and try to import it into Eclipse.  Can explain why if that would help.
 
Thanks for any help you can give me.  The Autoseg symposium you gave at the World Congress was very good.
 
Dave.
 
David Sasaki, M. Sc., MCCPM
CancerCare Manitoba
Winnipeg, MB
Canada
This email and/or any documents in this transmission is intended for the
addressee(s) only and may contain legally privileged or confidential information.  Any unauthorized use, disclosure, distribution, copying or dissemination is strictly prohibited.  If you receive this transmission in error, please notify the sender immediately and return the original.
Ce courriel et tout document dans cette transmission est destiné à la personne ou aux personnes à qui il est adressé. Il peut contenir des informations privilégiées ou confidentielles. Toute utilisation, divulgation, distribution, copie, ou diffusion non autorisée est strictement défendue. Si vous n'êtes pas le destinataire de ce message, veuillez en informer l'expéditeur immédiatement et lui remettre l'original.
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Re: 3D model to rtstruct. . .

Sharp, Gregory C.

Hi Dan,

 

That is a good question.  A bit outside my expertise.

 

Any Slicers know the answer(s)?

 

Greg

 

From: Dan Raviv [mailto:[hidden email]]
Sent: Tuesday, August 18, 2015 11:35 AM
To: Sharp, Gregory C.
Subject: Re: [slicer-users] 3D model to rtstruct. . .

 

Hi Gregory

I am a post-doc in MIT, working on 4D-CT data, and I am really impressed with Slicer. Great job.

 

I have a problem I hope you can help me regarding multiple-4D datasets. 

We have a 4D CT and an additional 4D information layer we generated.

I am importing the two sets using MultiVolumeImporter, and I can nicely visualize the results using MultiVolumeExplorer. But, only one volume is playing (in time) ! I could not find a way to do so for both simultaneously.

 

Assuming the answer “you can not do that”, then I thought to fuse the layers into one set. But I could not manage to load a (true) color 4D data into the system.

 

Any advice (for both options) ?

 

Thank you in advance

Dan

 

-------------------------------
Dan Raviv, PhD
Camera Culture Group,
Media Lab, MIT

 

 


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Re: 3D model to rtstruct. . .

Andras Lasso-2

VTK only supports volume rendering for one volume at a time, so you need to convert at least one of them to a model (surface mesh) using Grayscale model maker.

 

The MultiVolume module only supports replaying only volumes and max two volumes at a time. You need to install the Sequences extension and use the sequence browser to replay any kind of temporal sequence data. If you save the multi-volume CT as a nrrd file then you can load them into Slicer as Volume Sequence (in load data dialog you have to choose Volume Sequence in the description column). Unfortunately, you need to do the conversion to model manually or write a short Python script that iterates through the volume and creates the corresponding models. Let me know if you would like to try this workflow and you get stuck at any step.

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Sharp, Gregory C.
Sent: Tuesday, August 18, 2015 11:43 AM
To: 'Dan Raviv' <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] 3D model to rtstruct. . .

 

Hi Dan,

 

That is a good question.  A bit outside my expertise.

 

Any Slicers know the answer(s)?

 

Greg

 

From: Dan Raviv [[hidden email]]
Sent: Tuesday, August 18, 2015 11:35 AM
To: Sharp, Gregory C.
Subject: Re: [slicer-users] 3D model to rtstruct. . .

 

Hi Gregory

I am a post-doc in MIT, working on 4D-CT data, and I am really impressed with Slicer. Great job.

 

I have a problem I hope you can help me regarding multiple-4D datasets. 

We have a 4D CT and an additional 4D information layer we generated.

I am importing the two sets using MultiVolumeImporter, and I can nicely visualize the results using MultiVolumeExplorer. But, only one volume is playing (in time) ! I could not find a way to do so for both simultaneously.

 

Assuming the answer “you can not do that”, then I thought to fuse the layers into one set. But I could not manage to load a (true) color 4D data into the system.

 

Any advice (for both options) ?

 

Thank you in advance

Dan

 

-------------------------------
Dan Raviv, PhD
Camera Culture Group,
Media Lab, MIT

 

 


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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: 3D model to rtstruct. . .

Steve Pieper-2
Hi Dan - 

Going the Sequences route as Andras suggests will give you a lot of power, for example, to have fiducials or models per-time-point.

Another thing you might do in the mean time is merge the 4D CT with the 4D label to make one volume that can be rendered with the volume renderer.  E.g. you might mask the CT using the label, or otherwise enhance the part you want to see.

HTH,
Steve

On Tue, Aug 18, 2015 at 11:55 AM, Andras Lasso <[hidden email]> wrote:

VTK only supports volume rendering for one volume at a time, so you need to convert at least one of them to a model (surface mesh) using Grayscale model maker.

 

The MultiVolume module only supports replaying only volumes and max two volumes at a time. You need to install the Sequences extension and use the sequence browser to replay any kind of temporal sequence data. If you save the multi-volume CT as a nrrd file then you can load them into Slicer as Volume Sequence (in load data dialog you have to choose Volume Sequence in the description column). Unfortunately, you need to do the conversion to model manually or write a short Python script that iterates through the volume and creates the corresponding models. Let me know if you would like to try this workflow and you get stuck at any step.

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Sharp, Gregory C.
Sent: Tuesday, August 18, 2015 11:43 AM
To: 'Dan Raviv' <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] 3D model to rtstruct. . .

 

Hi Dan,

 

That is a good question.  A bit outside my expertise.

 

Any Slicers know the answer(s)?

 

Greg

 

From: Dan Raviv [[hidden email]]
Sent: Tuesday, August 18, 2015 11:35 AM
To: Sharp, Gregory C.
Subject: Re: [slicer-users] 3D model to rtstruct. . .

 

Hi Gregory

I am a post-doc in MIT, working on 4D-CT data, and I am really impressed with Slicer. Great job.

 

I have a problem I hope you can help me regarding multiple-4D datasets. 

We have a 4D CT and an additional 4D information layer we generated.

I am importing the two sets using MultiVolumeImporter, and I can nicely visualize the results using MultiVolumeExplorer. But, only one volume is playing (in time) ! I could not find a way to do so for both simultaneously.

 

Assuming the answer “you can not do that”, then I thought to fuse the layers into one set. But I could not manage to load a (true) color 4D data into the system.

 

Any advice (for both options) ?

 

Thank you in advance

Dan

 

-------------------------------
Dan Raviv, PhD
Camera Culture Group,
Media Lab, MIT

 

 


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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
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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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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.



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contains patient information, please contact the Partners Compliance HelpLine at
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Re: 3D model to rtstruct. . .

Andras Lasso-2
In reply to this post by Sharp, Gregory C.

 

1. Probably there is no way to replay even two volumes with MultiVolumeExplorer then

 

2. Use the nightly version of Slicer. Install Sequences extension. Drag-and-drop the 4D nrrd file into Slicer, choose Volume Sequence in the description column. Open the sequence browser module, click Play button. For simultaneous replay of multiple volumes: drag-and-drop additional volumes, in the sequence browser module click the checkboxes of all volumes that you would like to replay simultaneously.

 

3.

 

Merging the volumes is a good approach if the volumes are overlapping (this is what Steve suggested, too). This will work if you have for example a CT volume and some segmented structures; or two sets of segmented structures. I don’t think volume rendering of RGB of supported, so you would need to fuse the volumes in a way that you create a scalar output. You can start experimenting on a single pair of 3D volumes (one from each sequence) and use mean/minimum/maximum/etc operations (you can use SimpleFilters module or other modules in Filtering category).

 

Visualizing one CT using volume rendering and add segmented structures from the other CT may work nicely, too. It is simple to do as well, because you don’t need to fuse volumes.

 

Fusing two raw CT volumes (without segmentation) may give you somewhat usable results in 2D, but most likely the results won’t be good for any visualization in 3D.

 

Andras

 

 

From: Dan Raviv [mailto:[hidden email]]
Sent: Tuesday, August 18, 2015 12:27 PM
To: Andras Lasso <[hidden email]>
Subject: Re: [slicer-users] 3D model to rtstruct. . .

 

Hi Andras 

Thanks for the super fast reply!

 

I lost you.

 

1. The MultiVolumeExplorer allows us to play only *one* volume at a time. The secondary volume I can choose is only for the interactive chart.

 Is there a *quick* way to force the viewer to update both chosen volumes ?

 

2. I tried using sequences (which is is basically part of slicerRT), but I was not able to do that.

 Can you give a more detailed workflow ?

 

3. Maybe the simplest solution will be to store one *true color* 4D set. I could not do that as well. Any workflow for that ?

 

Just to be super clear:

I have a 4D cardiac CT (20 x volumes), and a second 4D images (20 x volumes) with content (not just labels).

I want to be able to play the scene with both volumes alter simultaneously.

 

Again, thank you for your help

Dan 

 

 

 

On Aug 18, 2015, at 11:55 AM, Andras Lasso <[hidden email]> wrote:

 

VTK only supports volume rendering for one volume at a time, so you need to convert at least one of them to a model (surface mesh) using Grayscale model maker.

 

The MultiVolume module only supports replaying only volumes and max two volumes at a time. You need to install the Sequences extension and use the sequence browser to replay any kind of temporal sequence data. If you save the multi-volume CT as a nrrd file then you can load them into Slicer as Volume Sequence (in load data dialog you have to choose Volume Sequence in the description column). Unfortunately, you need to do the conversion to model manually or write a short Python script that iterates through the volume and creates the corresponding models. Let me know if you would like to try this workflow and you get stuck at any step.

 

Andras

 

From: [hidden email] [[hidden email]] On Behalf Of Sharp, Gregory C.
Sent: Tuesday, August 18, 2015 11:43 AM
To: 'Dan Raviv' <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] 3D model to rtstruct. . .

 

Hi Dan,

 

That is a good question.  A bit outside my expertise.

 

Any Slicers know the answer(s)?

 

Greg

 

From: Dan Raviv [[hidden email]] 
Sent: Tuesday, August 18, 2015 11:35 AM
To: Sharp, Gregory C.
Subject: Re: [slicer-users] 3D model to rtstruct. . .

 

Hi Gregory

I am a post-doc in MIT, working on 4D-CT data, and I am really impressed with Slicer. Great job.

 

I have a problem I hope you can help me regarding multiple-4D datasets. 

We have a 4D CT and an additional 4D information layer we generated.

I am importing the two sets using MultiVolumeImporter, and I can nicely visualize the results using MultiVolumeExplorer. But, only one volume is playing (in time) ! I could not find a way to do so for both simultaneously.

 

Assuming the answer “you can not do that”, then I thought to fuse the layers into one set. But I could not manage to load a (true) color 4D data into the system.

 

Any advice (for both options) ?

 

Thank you in advance

Dan

 

-------------------------------
Dan Raviv, PhD
Camera Culture Group,
Media Lab, MIT 

 


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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: 3D model to rtstruct. . .

Steve Pieper-2
In reply to this post by Sharp, Gregory C.
Yes, I agree with Andras's suggestions.  Another idea might be to use the two threeD viewer layout option and make each volume visible in one of the viewers.  Then you could animate them side-by-side which might give you extra insight (again they would both need to be scalars).

Also you might get by with a pseudo color approach.  That is merge the two volumes but offset their intensities so that the base CT is, say, 0 to 1000 and the the overlay is 1000 to 2000.  Then use the lookup tables to give them different colors and opacities.

-Steve

On Tue, Aug 18, 2015 at 2:57 PM, Andras Lasso <[hidden email]> wrote:

 

1. Probably there is no way to replay even two volumes with MultiVolumeExplorer then

 

2. Use the nightly version of Slicer. Install Sequences extension. Drag-and-drop the 4D nrrd file into Slicer, choose Volume Sequence in the description column. Open the sequence browser module, click Play button. For simultaneous replay of multiple volumes: drag-and-drop additional volumes, in the sequence browser module click the checkboxes of all volumes that you would like to replay simultaneously.

 

3.

 

Merging the volumes is a good approach if the volumes are overlapping (this is what Steve suggested, too). This will work if you have for example a CT volume and some segmented structures; or two sets of segmented structures. I don’t think volume rendering of RGB of supported, so you would need to fuse the volumes in a way that you create a scalar output. You can start experimenting on a single pair of 3D volumes (one from each sequence) and use mean/minimum/maximum/etc operations (you can use SimpleFilters module or other modules in Filtering category).

 

Visualizing one CT using volume rendering and add segmented structures from the other CT may work nicely, too. It is simple to do as well, because you don’t need to fuse volumes.

 

Fusing two raw CT volumes (without segmentation) may give you somewhat usable results in 2D, but most likely the results won’t be good for any visualization in 3D.

 

Andras

 

 

From: Dan Raviv [mailto:[hidden email]]
Sent: Tuesday, August 18, 2015 12:27 PM
To: Andras Lasso <[hidden email]>
Subject: Re: [slicer-users] 3D model to rtstruct. . .

 

Hi Andras 

Thanks for the super fast reply!

 

I lost you.

 

1. The MultiVolumeExplorer allows us to play only *one* volume at a time. The secondary volume I can choose is only for the interactive chart.

 Is there a *quick* way to force the viewer to update both chosen volumes ?

 

2. I tried using sequences (which is is basically part of slicerRT), but I was not able to do that.

 Can you give a more detailed workflow ?

 

3. Maybe the simplest solution will be to store one *true color* 4D set. I could not do that as well. Any workflow for that ?

 

Just to be super clear:

I have a 4D cardiac CT (20 x volumes), and a second 4D images (20 x volumes) with content (not just labels).

I want to be able to play the scene with both volumes alter simultaneously.

 

Again, thank you for your help

Dan 

 

 

 

On Aug 18, 2015, at 11:55 AM, Andras Lasso <[hidden email]> wrote:

 

VTK only supports volume rendering for one volume at a time, so you need to convert at least one of them to a model (surface mesh) using Grayscale model maker.

 

The MultiVolume module only supports replaying only volumes and max two volumes at a time. You need to install the Sequences extension and use the sequence browser to replay any kind of temporal sequence data. If you save the multi-volume CT as a nrrd file then you can load them into Slicer as Volume Sequence (in load data dialog you have to choose Volume Sequence in the description column). Unfortunately, you need to do the conversion to model manually or write a short Python script that iterates through the volume and creates the corresponding models. Let me know if you would like to try this workflow and you get stuck at any step.

 

Andras

 

From: [hidden email] [[hidden email]] On Behalf Of Sharp, Gregory C.
Sent: Tuesday, August 18, 2015 11:43 AM
To: 'Dan Raviv' <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] 3D model to rtstruct. . .

 

Hi Dan,

 

That is a good question.  A bit outside my expertise.

 

Any Slicers know the answer(s)?

 

Greg

 

From: Dan Raviv [[hidden email]] 
Sent: Tuesday, August 18, 2015 11:35 AM
To: Sharp, Gregory C.
Subject: Re: [slicer-users] 3D model to rtstruct. . .

 

Hi Gregory

I am a post-doc in MIT, working on 4D-CT data, and I am really impressed with Slicer. Great job.

 

I have a problem I hope you can help me regarding multiple-4D datasets. 

We have a 4D CT and an additional 4D information layer we generated.

I am importing the two sets using MultiVolumeImporter, and I can nicely visualize the results using MultiVolumeExplorer. But, only one volume is playing (in time) ! I could not find a way to do so for both simultaneously.

 

Assuming the answer “you can not do that”, then I thought to fuse the layers into one set. But I could not manage to load a (true) color 4D data into the system.

 

Any advice (for both options) ?

 

Thank you in advance

Dan

 

-------------------------------
Dan Raviv, PhD
Camera Culture Group,
Media Lab, MIT 

 



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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
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
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