Re: Slicer to DICOM

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

Re: Slicer to DICOM

Csaba Pinter-2

Hi Elizabeth,

Only those objects can be exported to DICOM that have corresponding export plugins implemented. Currently there are no plugins handling model nodes to export. What DICOM modality do you want to export them to?

csaba

On October 2, 2015 3:26:30 PM "Mosher, Elizabeth (NIH/NCI) [F]" <[hidden email]> wrote:

Hi Csaba, 

I wanted to follow up with you about converting to DICOM files. I am able to right click under Subject Hierarchy. I have tried exporting the entire scene and only the CT images convert to DICOM files and not the .stl models I have created. I tried clicking on the .stl files individually as well and there is nothing listed under “2. Select export type” so it will not allow me to export. Do you have any suggestions?

Thanks,
Elizabeth 

From: Csaba Pinter <[hidden email]>
Date: Wednesday, September 16, 2015 at 3:02 PM
To: Elizabeth Mosher <[hidden email]>
Subject: RE: Slicer to DICOM

If you move your mouse on the CT image the HU value is shown in the bottom left.

 

csaba

 

From: Mosher, Elizabeth (NIH/NCI) [F] [[hidden email]]
Sent: September 16, 2015 14:59
To: Csaba Pinter <[hidden email]>
Subject: Re: Slicer to DICOM

 

Okay, thanks, I will let you know how it goes.

 

Is there a tool in 3D Slicer to detect the Hounsefield Unit at a specific location within a CT image?

 

Elizabeth

 

From: Csaba Pinter <[hidden email]>
Date: Wednesday, September 16, 2015 at 9:46 AM
To: Elizabeth Mosher <[hidden email]>
Subject: RE: Slicer to DICOM

 

Hi Elizabeth,

 

4.4.0 and nightly are two different versions. 4.4.0 is the stable that is almost a year old, and it has our own Contours module. The nightly is the cutting edge version that has our new Segmentations. You need to install SlicerRT to have that.

 

csaba

 

From: Mosher, Elizabeth (NIH/NCI) [F] [[hidden email]]
Sent: September 16, 2015 09:32
To: Csaba Pinter
Subject: Re: Slicer to DICOM

 

Hi Csaba, 

 

I did have one of the recent 4.4.0 nightly builds from the main 3D slicer website, but I downloaded the package from [3]. There does not seem to be a Segmentations module?

 

Elizabeth 

 

From: Csaba Pinter <[hidden email]>
Date: Tuesday, September 15, 2015 at 2:57 PM
To: Elizabeth Mosher <[hidden email]>
Subject: RE: Slicer to DICOM

 

Hi Elizabeth,

 

What Slicer version do you use? I suggest using a nightly (link 3 in my previous email).

 

You’ll have to create a subject, and within that a study. The CT and the Segmentation should be under that study. You can do all this in Subject hierarchy. Then if you right-click the study then you should able to export. The color of the structures can be changed in the Segmentations module, and this is where you can import models and labelmaps as “segments” to a segmentation.

 

csaba

 

From: Mosher, Elizabeth (NIH/NCI) [F] [[hidden email]]
Sent: September 15, 2015 14:53
To: Csaba Pinter
Subject: Re: Slicer to DICOM

 

Hi Csaba, 

 

Thank you for your response about DICOM export. I have not been able to get the DICOM export to work yet, but it may be because there is a problem with my slicer files. 

 

I have been working on contouring heart substructures based on CT images. I moved computers and copied my files on an external hard drive to transport them and now the mmrl scenes no longer open. I can load the CT images, the labels and the .stl files that I had, but I am not able to edit the structures because there is an error with the labels. The contours show up on the CT images, but on the per-structure volumes list the colors are all black and say invalid. The contours that show up on the CT images are different than their original colors (I used my own custom color file). Would you have any suggestions on what to do?

 

Thanks,

Elizabeth 

 

From: "Pyakuryal, Anil Prasad (NIH/NCI) [F]" <[hidden email]>
Date: Tuesday, September 8, 2015 at 2:39 PM
To: Csaba Pinter <[hidden email]>, "[hidden email]" <[hidden email]>
Cc: Elizabeth Mosher <[hidden email]>
Subject: RE: Slicer to DICOM

 

Thanks Csaba,

Our intern Elizabeth will carry on from there. I checked my old files and saw that dicom rt structure was indeed exported in 3D Slicer a few years ago. So it should be possible. Thanks Csaba.

- Anil


From: Csaba Pinter [[hidden email]]
Sent: Tuesday, September 08, 2015 2:33 PM
To: Pyakuryal, Anil Prasad (NIH/NCI) [F]; [hidden email]
Cc: Mosher, Elizabeth (NIH/NCI) [F]
Subject: RE: Slicer to DICOM

Hi Anil,

 

Not sure why you attached the tutorial file, but it is 2 years old, which is an eternity in software development (there is a newer one that you can find in the SlicerRT user documentation [1], but it does not include exporting).

 

Indeed, there is a “direct way” in Slicer to export DICOM-RT. It will work from a nightly build (maybe also 4.4, but not sure; also please note that 4.5 is coming soon, the deadline is Nov 2). Today’s nighty for Windows can be downloaded from here [2], if you need Mac or Linux, then click the package icons next to the platform here [3].

 

You can do it from Subject hierarchy, or the DICOM browser, both lead to the same DICOM export window. Please read this page

http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DICOMExport

and let me know if there are any questions, or if you succeeded.

 

Thanks,

csaba

 

[1] http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT

[2] http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.4.0-2015-09-04-win-amd64.exe&checksum=ce6c5a87b9be437b588f6b497186c4f3

[3] http://slicer.cdash.org/index.php?project=Slicer4&display=project

 

From: Pyakuryal, Anil Prasad (NIH/NCI) [F] [[hidden email]]
Sent: September 8, 2015 14:26
To: [hidden email]
Cc: Mosher, Elizabeth (NIH/NCI) [F] <[hidden email]>
Subject: RE: Slicer to DICOM

 

Csaba,

Could you ps provide a quick way out to export the rt structure dicom file from dico_rt plan in 3D Slicer to us. I know its possible though there is no direct way out for this in Slicer currently. Thanks Csaba for help.

-Anil


From: Mosher, Elizabeth (NIH/NCI) [F]
Sent: Tuesday, September 08, 2015 2:05 PM
To: Pyakuryal, Anil Prasad (NIH/NCI) [F]
Subject: Slicer to DICOM

Hi Anil, 

 

Have you ever exported a scene from Slicer as DICOM structure files?

 

Elizabeth 


_______________________________________________
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: Slicer to DICOM

Andrey Fedorov-2
Elizabeth,

would also be helpful if you could explain why you want to export them
to DICOM, what exactly you are trying to accomplish with the result of
that export?

AF



On Fri, Oct 2, 2015 at 3:42 PM, Csaba Pinter <[hidden email]> wrote:

> Hi Elizabeth,
>
> Only those objects can be exported to DICOM that have corresponding export
> plugins implemented. Currently there are no plugins handling model nodes to
> export. What DICOM modality do you want to export them to?
>
> csaba
>
> On October 2, 2015 3:26:30 PM "Mosher, Elizabeth (NIH/NCI) [F]"
> <[hidden email]> wrote:
>>
>> Hi Csaba,
>>
>> I wanted to follow up with you about converting to DICOM files. I am able
>> to right click under Subject Hierarchy. I have tried exporting the entire
>> scene and only the CT images convert to DICOM files and not the .stl models
>> I have created. I tried clicking on the .stl files individually as well and
>> there is nothing listed under “2. Select export type” so it will not allow
>> me to export. Do you have any suggestions?
>>
>> Thanks,
>> Elizabeth
>>
>> From: Csaba Pinter <[hidden email]>
>> Date: Wednesday, September 16, 2015 at 3:02 PM
>> To: Elizabeth Mosher <[hidden email]>
>> Subject: RE: Slicer to DICOM
>>
>> If you move your mouse on the CT image the HU value is shown in the bottom
>> left.
>>
>>
>>
>> csaba
>>
>>
>>
>> From: Mosher, Elizabeth (NIH/NCI) [F] [mailto:[hidden email]]
>> Sent: September 16, 2015 14:59
>> To: Csaba Pinter <[hidden email]>
>> Subject: Re: Slicer to DICOM
>>
>>
>>
>> Okay, thanks, I will let you know how it goes.
>>
>>
>>
>> Is there a tool in 3D Slicer to detect the Hounsefield Unit at a specific
>> location within a CT image?
>>
>>
>>
>> Elizabeth
>>
>>
>>
>> From: Csaba Pinter <[hidden email]>
>> Date: Wednesday, September 16, 2015 at 9:46 AM
>> To: Elizabeth Mosher <[hidden email]>
>> Subject: RE: Slicer to DICOM
>>
>>
>>
>> Hi Elizabeth,
>>
>>
>>
>> 4.4.0 and nightly are two different versions. 4.4.0 is the stable that is
>> almost a year old, and it has our own Contours module. The nightly is the
>> cutting edge version that has our new Segmentations. You need to install
>> SlicerRT to have that.
>>
>>
>>
>> csaba
>>
>>
>>
>> From: Mosher, Elizabeth (NIH/NCI) [F] [mailto:[hidden email]]
>> Sent: September 16, 2015 09:32
>> To: Csaba Pinter
>> Subject: Re: Slicer to DICOM
>>
>>
>>
>> Hi Csaba,
>>
>>
>>
>> I did have one of the recent 4.4.0 nightly builds from the main 3D slicer
>> website, but I downloaded the package from [3]. There does not seem to be a
>> Segmentations module?
>>
>>
>>
>> Elizabeth
>>
>>
>>
>> From: Csaba Pinter <[hidden email]>
>> Date: Tuesday, September 15, 2015 at 2:57 PM
>> To: Elizabeth Mosher <[hidden email]>
>> Subject: RE: Slicer to DICOM
>>
>>
>>
>> Hi Elizabeth,
>>
>>
>>
>> What Slicer version do you use? I suggest using a nightly (link 3 in my
>> previous email).
>>
>>
>>
>> You’ll have to create a subject, and within that a study. The CT and the
>> Segmentation should be under that study. You can do all this in Subject
>> hierarchy. Then if you right-click the study then you should able to export.
>> The color of the structures can be changed in the Segmentations module, and
>> this is where you can import models and labelmaps as “segments” to a
>> segmentation.
>>
>>
>>
>> csaba
>>
>>
>>
>> From: Mosher, Elizabeth (NIH/NCI) [F] [mailto:[hidden email]]
>> Sent: September 15, 2015 14:53
>> To: Csaba Pinter
>> Subject: Re: Slicer to DICOM
>>
>>
>>
>> Hi Csaba,
>>
>>
>>
>> Thank you for your response about DICOM export. I have not been able to
>> get the DICOM export to work yet, but it may be because there is a problem
>> with my slicer files.
>>
>>
>>
>> I have been working on contouring heart substructures based on CT images.
>> I moved computers and copied my files on an external hard drive to transport
>> them and now the mmrl scenes no longer open. I can load the CT images, the
>> labels and the .stl files that I had, but I am not able to edit the
>> structures because there is an error with the labels. The contours show up
>> on the CT images, but on the per-structure volumes list the colors are all
>> black and say invalid. The contours that show up on the CT images are
>> different than their original colors (I used my own custom color file).
>> Would you have any suggestions on what to do?
>>
>>
>>
>> Thanks,
>>
>> Elizabeth
>>
>>
>>
>> From: "Pyakuryal, Anil Prasad (NIH/NCI) [F]"
>> <[hidden email]>
>> Date: Tuesday, September 8, 2015 at 2:39 PM
>> To: Csaba Pinter <[hidden email]>, "[hidden email]"
>> <[hidden email]>
>> Cc: Elizabeth Mosher <[hidden email]>
>> Subject: RE: Slicer to DICOM
>>
>>
>>
>> Thanks Csaba,
>>
>> Our intern Elizabeth will carry on from there. I checked my old files and
>> saw that dicom rt structure was indeed exported in 3D Slicer a few years
>> ago. So it should be possible. Thanks Csaba.
>>
>> - Anil
>>
>> ________________________________
>>
>> From: Csaba Pinter [[hidden email]]
>> Sent: Tuesday, September 08, 2015 2:33 PM
>> To: Pyakuryal, Anil Prasad (NIH/NCI) [F]; [hidden email]
>> Cc: Mosher, Elizabeth (NIH/NCI) [F]
>> Subject: RE: Slicer to DICOM
>>
>> Hi Anil,
>>
>>
>>
>> Not sure why you attached the tutorial file, but it is 2 years old, which
>> is an eternity in software development (there is a newer one that you can
>> find in the SlicerRT user documentation [1], but it does not include
>> exporting).
>>
>>
>>
>> Indeed, there is a “direct way” in Slicer to export DICOM-RT. It will work
>> from a nightly build (maybe also 4.4, but not sure; also please note that
>> 4.5 is coming soon, the deadline is Nov 2). Today’s nighty for Windows can
>> be downloaded from here [2], if you need Mac or Linux, then click the
>> package icons next to the platform here [3].
>>
>>
>>
>> You can do it from Subject hierarchy, or the DICOM browser, both lead to
>> the same DICOM export window. Please read this page
>>
>> http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DICOMExport
>>
>> and let me know if there are any questions, or if you succeeded.
>>
>>
>>
>> Thanks,
>>
>> csaba
>>
>>
>>
>> [1]
>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT
>>
>> [2]
>> http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.4.0-2015-09-04-win-amd64.exe&checksum=ce6c5a87b9be437b588f6b497186c4f3
>>
>> [3] http://slicer.cdash.org/index.php?project=Slicer4&display=project
>>
>>
>>
>> From: Pyakuryal, Anil Prasad (NIH/NCI) [F]
>> [mailto:[hidden email]]
>> Sent: September 8, 2015 14:26
>> To: [hidden email]
>> Cc: Mosher, Elizabeth (NIH/NCI) [F] <[hidden email]>
>> Subject: RE: Slicer to DICOM
>>
>>
>>
>> Csaba,
>>
>> Could you ps provide a quick way out to export the rt structure dicom file
>> from dico_rt plan in 3D Slicer to us. I know its possible though there is no
>> direct way out for this in Slicer currently. Thanks Csaba for help.
>>
>> -Anil
>>
>> ________________________________
>>
>> From: Mosher, Elizabeth (NIH/NCI) [F]
>> Sent: Tuesday, September 08, 2015 2:05 PM
>> To: Pyakuryal, Anil Prasad (NIH/NCI) [F]
>> Subject: Slicer to DICOM
>>
>> Hi Anil,
>>
>>
>>
>> Have you ever exported a scene from Slicer as DICOM structure files?
>>
>>
>>
>> Elizabeth
>
>
> _______________________________________________
> 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: Slicer to DICOM

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

Hi Elizabeth,

 

You can export both models and labelmaps to DICOM RTSS. The difference is that if your segmentation contains models, then they are converted to labelmaps and the contour control points are extracted from those.

 

You need to add the Segmentation node [1] under a study [2] (which should be under a patient), and you can export it using the DICOM export functionality [3].

 

Where do your models come from? Actual STL files?

 

csaba

 

[1] http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Segmentations

[2] http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/SubjectHierarchy

[3] http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DICOMExport

 

From: Mosher, Elizabeth (NIH/NCI) [F] [mailto:[hidden email]]
Sent: October 5, 2015 15:26
To: Csaba Pinter <[hidden email]>
Subject: Re: Slicer to DICOM

 

Hi Csaba, 

 

I wanted to export them to DICOM RT structure files. If it is possible to export the label maps (the contours) instead of the .stl files to DICOM RT structures files then that would work too. The contours I have made in Slicer need to be opened by a radiotherapy treatment planning system which recognizes DICOM files. We plan to use these files to calculate heart dose during radiation cancer treatments. 

 

Elizabeth

 

From: Csaba Pinter <[hidden email]>
Date: Friday, October 2, 2015 at 3:42 PM
To: Elizabeth Mosher <[hidden email]>, Slicer Users Mailing List <[hidden email]>
Subject: Re: Slicer to DICOM

 

Hi Elizabeth,

Only those objects can be exported to DICOM that have corresponding export plugins implemented. Currently there are no plugins handling model nodes to export. What DICOM modality do you want to export them to?

csaba

On October 2, 2015 3:26:30 PM "Mosher, Elizabeth (NIH/NCI) [F]" <[hidden email]> wrote:

Hi Csaba, 

 

I wanted to follow up with you about converting to DICOM files. I am able to right click under Subject Hierarchy. I have tried exporting the entire scene and only the CT images convert to DICOM files and not the .stl models I have created. I tried clicking on the .stl files individually as well and there is nothing listed under “2. Select export type” so it will not allow me to export. Do you have any suggestions?

 

Thanks,

Elizabeth 

 

From: Csaba Pinter <[hidden email]>
Date: Wednesday, September 16, 2015 at 3:02 PM
To: Elizabeth Mosher <[hidden email]>
Subject: RE: Slicer to DICOM

 

If you move your mouse on the CT image the HU value is shown in the bottom left.

 

csaba

 

From: Mosher, Elizabeth (NIH/NCI) [F] [[hidden email]]
Sent: September 16, 2015 14:59
To: Csaba Pinter <[hidden email]>
Subject: Re: Slicer to DICOM

 

Okay, thanks, I will let you know how it goes.

 

Is there a tool in 3D Slicer to detect the Hounsefield Unit at a specific location within a CT image?

 

Elizabeth

 

From: Csaba Pinter <[hidden email]>
Date: Wednesday, September 16, 2015 at 9:46 AM
To: Elizabeth Mosher <[hidden email]>
Subject: RE: Slicer to DICOM

 

Hi Elizabeth,

 

4.4.0 and nightly are two different versions. 4.4.0 is the stable that is almost a year old, and it has our own Contours module. The nightly is the cutting edge version that has our new Segmentations. You need to install SlicerRT to have that.

 

csaba

 

From: Mosher, Elizabeth (NIH/NCI) [F] [[hidden email]]
Sent: September 16, 2015 09:32
To: Csaba Pinter
Subject: Re: Slicer to DICOM

 

Hi Csaba, 

 

I did have one of the recent 4.4.0 nightly builds from the main 3D slicer website, but I downloaded the package from [3]. There does not seem to be a Segmentations module?

 

Elizabeth 

 

From: Csaba Pinter <[hidden email]>
Date: Tuesday, September 15, 2015 at 2:57 PM
To: Elizabeth Mosher <[hidden email]>
Subject: RE: Slicer to DICOM

 

Hi Elizabeth,

 

What Slicer version do you use? I suggest using a nightly (link 3 in my previous email).

 

You’ll have to create a subject, and within that a study. The CT and the Segmentation should be under that study. You can do all this in Subject hierarchy. Then if you right-click the study then you should able to export. The color of the structures can be changed in the Segmentations module, and this is where you can import models and labelmaps as “segments” to a segmentation.

 

csaba

 

From: Mosher, Elizabeth (NIH/NCI) [F] [[hidden email]]
Sent: September 15, 2015 14:53
To: Csaba Pinter
Subject: Re: Slicer to DICOM

 

Hi Csaba, 

 

Thank you for your response about DICOM export. I have not been able to get the DICOM export to work yet, but it may be because there is a problem with my slicer files. 

 

I have been working on contouring heart substructures based on CT images. I moved computers and copied my files on an external hard drive to transport them and now the mmrl scenes no longer open. I can load the CT images, the labels and the .stl files that I had, but I am not able to edit the structures because there is an error with the labels. The contours show up on the CT images, but on the per-structure volumes list the colors are all black and say invalid. The contours that show up on the CT images are different than their original colors (I used my own custom color file). Would you have any suggestions on what to do?

 

Thanks,

Elizabeth 

 

From: "Pyakuryal, Anil Prasad (NIH/NCI) [F]" <[hidden email]>
Date: Tuesday, September 8, 2015 at 2:39 PM
To: Csaba Pinter <[hidden email]>, "[hidden email]" <[hidden email]>
Cc: Elizabeth Mosher <[hidden email]>
Subject: RE: Slicer to DICOM

 

Thanks Csaba,

Our intern Elizabeth will carry on from there. I checked my old files and saw that dicom rt structure was indeed exported in 3D Slicer a few years ago. So it should be possible. Thanks Csaba.

- Anil


From: Csaba Pinter [[hidden email]]
Sent: Tuesday, September 08, 2015 2:33 PM
To: Pyakuryal, Anil Prasad (NIH/NCI) [F]; [hidden email]
Cc: Mosher, Elizabeth (NIH/NCI) [F]
Subject: RE: Slicer to DICOM

Hi Anil,

 

Not sure why you attached the tutorial file, but it is 2 years old, which is an eternity in software development (there is a newer one that you can find in the SlicerRT user documentation [1], but it does not include exporting).

 

Indeed, there is a “direct way” in Slicer to export DICOM-RT. It will work from a nightly build (maybe also 4.4, but not sure; also please note that 4.5 is coming soon, the deadline is Nov 2). Today’s nighty for Windows can be downloaded from here [2], if you need Mac or Linux, then click the package icons next to the platform here [3].

 

You can do it from Subject hierarchy, or the DICOM browser, both lead to the same DICOM export window. Please read this page

http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DICOMExport

and let me know if there are any questions, or if you succeeded.

 

Thanks,

csaba

 

[1] http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT

[2] http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.4.0-2015-09-04-win-amd64.exe&checksum=ce6c5a87b9be437b588f6b497186c4f3

[3] http://slicer.cdash.org/index.php?project=Slicer4&display=project

 

From: Pyakuryal, Anil Prasad (NIH/NCI) [F] [[hidden email]]
Sent: September 8, 2015 14:26
To: [hidden email]
Cc: Mosher, Elizabeth (NIH/NCI) [F] <[hidden email]>
Subject: RE: Slicer to DICOM

 

Csaba,

Could you ps provide a quick way out to export the rt structure dicom file from dico_rt plan in 3D Slicer to us. I know its possible though there is no direct way out for this in Slicer currently. Thanks Csaba for help.

-Anil


From: Mosher, Elizabeth (NIH/NCI) [F]
Sent: Tuesday, September 08, 2015 2:05 PM
To: Pyakuryal, Anil Prasad (NIH/NCI) [F]
Subject: Slicer to DICOM

Hi Anil, 

 

Have you ever exported a scene from Slicer as DICOM structure files?

 

Elizabeth 


_______________________________________________
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: Slicer to DICOM

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

Hi Elizabeth,

 

Is there a specific reason for converting the labelmaps (that you create in Editor) to models? If you need to export them to RTSS then you can just create the segmentations from the labelmaps and export them.

You can use the import function of the Segmentations module to add the segments (structures) to the segmentation node (structure set). You need this node in order to export them to RTSS.

 

csaba

 

From: Mosher, Elizabeth (NIH/NCI) [F] [mailto:[hidden email]]
Sent: October 5, 2015 16:05
To: Csaba Pinter <[hidden email]>
Subject: Re: Slicer to DICOM

 

Okay, thank you, I will look into this. 

 

The models (stl files) I created in the Editor Module in Slicer from the label maps. 

 

Elizabeth

 

From: Csaba Pinter <[hidden email]>
Date: Monday, October 5, 2015 at 3:33 PM
To: Elizabeth Mosher <[hidden email]>
Cc: "Slicer Users Mailing List ([hidden email])" <[hidden email]>
Subject: RE: Slicer to DICOM

 

Hi Elizabeth,

 

You can export both models and labelmaps to DICOM RTSS. The difference is that if your segmentation contains models, then they are converted to labelmaps and the contour control points are extracted from those.

 

You need to add the Segmentation node [1] under a study [2] (which should be under a patient), and you can export it using the DICOM export functionality [3].

 

Where do your models come from? Actual STL files?

 

csaba

 

[1] http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Segmentations

[2] http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/SubjectHierarchy

[3] http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DICOMExport

 

From: Mosher, Elizabeth (NIH/NCI) [F] [[hidden email]]
Sent: October 5, 2015 15:26
To: Csaba Pinter <[hidden email]>
Subject: Re: Slicer to DICOM

 

Hi Csaba, 

 

I wanted to export them to DICOM RT structure files. If it is possible to export the label maps (the contours) instead of the .stl files to DICOM RT structures files then that would work too. The contours I have made in Slicer need to be opened by a radiotherapy treatment planning system which recognizes DICOM files. We plan to use these files to calculate heart dose during radiation cancer treatments. 

 

Elizabeth

 

From: Csaba Pinter <[hidden email]>
Date: Friday, October 2, 2015 at 3:42 PM
To: Elizabeth Mosher <[hidden email]>, Slicer Users Mailing List <[hidden email]>
Subject: Re: Slicer to DICOM

 

Hi Elizabeth,

Only those objects can be exported to DICOM that have corresponding export plugins implemented. Currently there are no plugins handling model nodes to export. What DICOM modality do you want to export them to?

csaba

On October 2, 2015 3:26:30 PM "Mosher, Elizabeth (NIH/NCI) [F]" <[hidden email]> wrote:

Hi Csaba, 

 

I wanted to follow up with you about converting to DICOM files. I am able to right click under Subject Hierarchy. I have tried exporting the entire scene and only the CT images convert to DICOM files and not the .stl models I have created. I tried clicking on the .stl files individually as well and there is nothing listed under “2. Select export type” so it will not allow me to export. Do you have any suggestions?

 

Thanks,

Elizabeth 

 

From: Csaba Pinter <[hidden email]>
Date: Wednesday, September 16, 2015 at 3:02 PM
To: Elizabeth Mosher <[hidden email]>
Subject: RE: Slicer to DICOM

 

If you move your mouse on the CT image the HU value is shown in the bottom left.

 

csaba

 

From: Mosher, Elizabeth (NIH/NCI) [F] [[hidden email]]
Sent: September 16, 2015 14:59
To: Csaba Pinter <[hidden email]>
Subject: Re: Slicer to DICOM

 

Okay, thanks, I will let you know how it goes.

 

Is there a tool in 3D Slicer to detect the Hounsefield Unit at a specific location within a CT image?

 

Elizabeth

 

From: Csaba Pinter <[hidden email]>
Date: Wednesday, September 16, 2015 at 9:46 AM
To: Elizabeth Mosher <[hidden email]>
Subject: RE: Slicer to DICOM

 

Hi Elizabeth,

 

4.4.0 and nightly are two different versions. 4.4.0 is the stable that is almost a year old, and it has our own Contours module. The nightly is the cutting edge version that has our new Segmentations. You need to install SlicerRT to have that.

 

csaba

 

From: Mosher, Elizabeth (NIH/NCI) [F] [[hidden email]]
Sent: September 16, 2015 09:32
To: Csaba Pinter
Subject: Re: Slicer to DICOM

 

Hi Csaba, 

 

I did have one of the recent 4.4.0 nightly builds from the main 3D slicer website, but I downloaded the package from [3]. There does not seem to be a Segmentations module?

 

Elizabeth 

 

From: Csaba Pinter <[hidden email]>
Date: Tuesday, September 15, 2015 at 2:57 PM
To: Elizabeth Mosher <[hidden email]>
Subject: RE: Slicer to DICOM

 

Hi Elizabeth,

 

What Slicer version do you use? I suggest using a nightly (link 3 in my previous email).

 

You’ll have to create a subject, and within that a study. The CT and the Segmentation should be under that study. You can do all this in Subject hierarchy. Then if you right-click the study then you should able to export. The color of the structures can be changed in the Segmentations module, and this is where you can import models and labelmaps as “segments” to a segmentation.

 

csaba

 

From: Mosher, Elizabeth (NIH/NCI) [F] [[hidden email]]
Sent: September 15, 2015 14:53
To: Csaba Pinter
Subject: Re: Slicer to DICOM

 

Hi Csaba, 

 

Thank you for your response about DICOM export. I have not been able to get the DICOM export to work yet, but it may be because there is a problem with my slicer files. 

 

I have been working on contouring heart substructures based on CT images. I moved computers and copied my files on an external hard drive to transport them and now the mmrl scenes no longer open. I can load the CT images, the labels and the .stl files that I had, but I am not able to edit the structures because there is an error with the labels. The contours show up on the CT images, but on the per-structure volumes list the colors are all black and say invalid. The contours that show up on the CT images are different than their original colors (I used my own custom color file). Would you have any suggestions on what to do?

 

Thanks,

Elizabeth 

 

From: "Pyakuryal, Anil Prasad (NIH/NCI) [F]" <[hidden email]>
Date: Tuesday, September 8, 2015 at 2:39 PM
To: Csaba Pinter <[hidden email]>, "[hidden email]" <[hidden email]>
Cc: Elizabeth Mosher <[hidden email]>
Subject: RE: Slicer to DICOM

 

Thanks Csaba,

Our intern Elizabeth will carry on from there. I checked my old files and saw that dicom rt structure was indeed exported in 3D Slicer a few years ago. So it should be possible. Thanks Csaba.

- Anil


From: Csaba Pinter [[hidden email]]
Sent: Tuesday, September 08, 2015 2:33 PM
To: Pyakuryal, Anil Prasad (NIH/NCI) [F]; [hidden email]
Cc: Mosher, Elizabeth (NIH/NCI) [F]
Subject: RE: Slicer to DICOM

Hi Anil,

 

Not sure why you attached the tutorial file, but it is 2 years old, which is an eternity in software development (there is a newer one that you can find in the SlicerRT user documentation [1], but it does not include exporting).

 

Indeed, there is a “direct way” in Slicer to export DICOM-RT. It will work from a nightly build (maybe also 4.4, but not sure; also please note that 4.5 is coming soon, the deadline is Nov 2). Today’s nighty for Windows can be downloaded from here [2], if you need Mac or Linux, then click the package icons next to the platform here [3].

 

You can do it from Subject hierarchy, or the DICOM browser, both lead to the same DICOM export window. Please read this page

http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DICOMExport

and let me know if there are any questions, or if you succeeded.

 

Thanks,

csaba

 

[1] http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT

[2] http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.4.0-2015-09-04-win-amd64.exe&checksum=ce6c5a87b9be437b588f6b497186c4f3

[3] http://slicer.cdash.org/index.php?project=Slicer4&display=project

 

From: Pyakuryal, Anil Prasad (NIH/NCI) [F] [[hidden email]]
Sent: September 8, 2015 14:26
To: [hidden email]
Cc: Mosher, Elizabeth (NIH/NCI) [F] <[hidden email]>
Subject: RE: Slicer to DICOM

 

Csaba,

Could you ps provide a quick way out to export the rt structure dicom file from dico_rt plan in 3D Slicer to us. I know its possible though there is no direct way out for this in Slicer currently. Thanks Csaba for help.

-Anil


From: Mosher, Elizabeth (NIH/NCI) [F]
Sent: Tuesday, September 08, 2015 2:05 PM
To: Pyakuryal, Anil Prasad (NIH/NCI) [F]
Subject: Slicer to DICOM

Hi Anil, 

 

Have you ever exported a scene from Slicer as DICOM structure files?

 

Elizabeth 


_______________________________________________
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.