Contouring for Radiotherapy application

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Contouring for Radiotherapy application

Devakumar-2
Dear Slicer group

I would like to contour tumor and organs from the CT or MRI, convert
contours into DICOM RT structures and transfer to Radiotherapy reatment
planning system. The segmentation modules in Slicer are not giving contours.
Please help me.

Best regards
Devakumar


----------------------------------------------------------------------------
-------------------------
Devakumar, Ph.D., D.R.P.
Department of Nuclear Medicine
Christian Medical College
Vellore, India
Phone: +91 9994206171
----------------------------------------------------------------------------
-------------------------



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Re: Contouring for Radiotherapy application

Sharp, Gregory C.
Hi Devakumar
 
At this time, it is still very difficult to create DICOM RT contours
using the Slicer editor.  
 
For a single structure you can probably use the plastimatch DICOM-RT
export function.  You might even be able to get multiple non-overlapping
structures to work too.  If you want to try this, be sure to use structure
numbers which are a power of two: 1, 2, 4, 8, ...
 
Greg
 
________________________________

From: [hidden email] on behalf of Devakumar
Sent: Thu 6/16/2011 10:59 PM
To: [hidden email]
Subject: [slicer-users] Contouring for Radiotherapy application



Dear Slicer group

I would like to contour tumor and organs from the CT or MRI, convert
contours into DICOM RT structures and transfer to Radiotherapy reatment
planning system. The segmentation modules in Slicer are not giving contours.
Please help me.

Best regards
Devakumar


----------------------------------------------------------------------------
-------------------------
Devakumar, Ph.D., D.R.P.
Department of Nuclear Medicine
Christian Medical College
Vellore, India
Phone: +91 9994206171
----------------------------------------------------------------------------
-------------------------



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slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with
unsubscribe as the subject


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Re: Contouring for Radiotherapy application

madanrao
Hello Dr.Devakumar,

Slicer3 automatic segmentation module can segment brain and abdominal organs for whom atlas templates are available. Over all shape and 3D alignments are preserved. It can also run from commandline and is amenable for batch processing (meaning you can run many CT images at a time). Tumors need to be manually segmented (as they are not represented in the atlas). The models align when
superimposed on original DICOM images.

The entire process is well documented by Pohl in his thesis on brain parcellation. However, I think it is somewhat difficult technically
and not easily implementable.

Best regards,

AM Mohan Rao

On Fri, Jun 17, 2011 at 9:16 AM, Sharp, Gregory C. <[hidden email]> wrote:
Hi Devakumar

At this time, it is still very difficult to create DICOM RT contours
using the Slicer editor.

For a single structure you can probably use the plastimatch DICOM-RT
export function.  You might even be able to get multiple non-overlapping
structures to work too.  If you want to try this, be sure to use structure
numbers which are a power of two: 1, 2, 4, 8, ...

Greg

________________________________

From: [hidden email] on behalf of Devakumar
Sent: Thu 6/16/2011 10:59 PM
To: [hidden email]
Subject: [slicer-users] Contouring for Radiotherapy application



Dear Slicer group

I would like to contour tumor and organs from the CT or MRI, convert
contours into DICOM RT structures and transfer to Radiotherapy reatment
planning system. The segmentation modules in Slicer are not giving contours.
Please help me.

Best regards
Devakumar


----------------------------------------------------------------------------
-------------------------
Devakumar, Ph.D., D.R.P.
Department of Nuclear Medicine
Christian Medical College
Vellore, India
Phone: +91 9994206171
----------------------------------------------------------------------------
-------------------------



_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with
unsubscribe as the subject


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[hidden email]
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Re: Contouring for Radiotherapy application

Devakumar-2
In reply to this post by Sharp, Gregory C.
Dear Greg

Thank you. I installed Slicer from the binary file
"Slicer3-3.6.4-beta-2011-06-10-win32.exe". I used extension manager to add
the plastimatch. I could not see any plastimatch modules (like DICOM RT
Import Export) in Slicer after the installation of extension. There is a
module called "Polydata to Labelmap" that may belong to plastimatch but I am
not sure it can help in any way to get contours in DICOM RT structure
format.

Thanks
Devakumar

-----Original Message-----
From: Sharp, Gregory C. [mailto:[hidden email]]
Sent: Friday, June 17, 2011 9:17 AM
To: Devakumar; [hidden email]
Subject: RE: [slicer-users] Contouring for Radiotherapy application

Hi Devakumar
 
At this time, it is still very difficult to create DICOM RT contours
using the Slicer editor.  
 
For a single structure you can probably use the plastimatch DICOM-RT
export function.  You might even be able to get multiple non-overlapping
structures to work too.  If you want to try this, be sure to use structure
numbers which are a power of two: 1, 2, 4, 8, ...
 
Greg
 
________________________________

From: [hidden email] on behalf of Devakumar
Sent: Thu 6/16/2011 10:59 PM
To: [hidden email]
Subject: [slicer-users] Contouring for Radiotherapy application



Dear Slicer group

I would like to contour tumor and organs from the CT or MRI, convert
contours into DICOM RT structures and transfer to Radiotherapy reatment
planning system. The segmentation modules in Slicer are not giving contours.
Please help me.

Best regards
Devakumar


----------------------------------------------------------------------------
-------------------------
Devakumar, Ph.D., D.R.P.
Department of Nuclear Medicine
Christian Medical College
Vellore, India
Phone: +91 9994206171
----------------------------------------------------------------------------
-------------------------



_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email]
with
unsubscribe as the subject




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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: Contouring for Radiotherapy application

Devakumar-2
In reply to this post by Devakumar-2
Dear Dr. Mohan Rao and slicer group
       
Thank you. Yes, I have tried EM Segmentation for brain based on atlas. It
works well. But for Radiotherapy applications I need to convert the
segmented regions into contours and then to DICOM-RT Structure format.
Kitware group has developed some code which can be used in ITK, but not on
Slicer. I have not yet tried that. I assume these segmented regions can be
saved as label map or models and can be used in ITK for conversion of mask
and contour as suggested by ITK group. Please share your experience.

Best regards
Devakumar

Date: Fri, 17 Jun 2011 10:25:52 +0530
From: Madan Rao <[hidden email]>
Subject: Re: [slicer-users] Contouring for Radiotherapy application
To: [hidden email]
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"

Hello Dr.Devakumar,

Slicer3 automatic segmentation module can segment brain and abdominal organs
for whom atlas templates are available. Over all shape and 3D alignments are
preserved. It can also run from commandline and is amenable for batch
processing (meaning you can run many CT images at a time). Tumors need to be
manually segmented (as they are not represented in the atlas). The models
align when superimposed on original DICOM images.

The entire process is well documented by Pohl in his thesis on brain
parcellation. However, I think it is somewhat difficult technically and not
easily implementable.

Best regards,

AM Mohan Rao

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Re: Contouring for Radiotherapy application

Sharp, Gregory C.
In reply to this post by Devakumar-2
Hi Devakumar,
 
The plastimatch modules will show up near the bottom of the
modules dropdown list.  They are all in their own "Plastimatch" group.
Within Plastimatch group should be a menu item "DICOM / DICOM-RT
Export".
 
If the extension installed properly, you should see the following:
 
(1) The extension install directory is added to the slicer module search
path.  Go to View -> Application Settings -> Module Settings, and
you will find the list of directores where modules are searched.
 
On Windows 7, the extension install directory looks like this:

C:/Users/gcs6/AppData/Local/Temp/Slicer3/@SVN@/plastimatch-slicer
 
For the @SVN@ part, you will need to replace with the Slicer svn version,
which is probably something like "16156".
 
(2) The extension files, such as plastimatch_slicer_dicomrt_export.exe,
are located in your extension install directory.
 
So I suggest to check the above items, see if everything got installed
correctly.
 
Greg
 
________________________________

From: Devakumar [mailto:[hidden email]]
Sent: Fri 6/17/2011 1:14 AM
To: Sharp, Gregory C.; [hidden email]
Subject: RE: Contouring for Radiotherapy application



Dear Greg

Thank you. I installed Slicer from the binary file
"Slicer3-3.6.4-beta-2011-06-10-win32.exe". I used extension manager to add
the plastimatch. I could not see any plastimatch modules (like DICOM RT
Import Export) in Slicer after the installation of extension. There is a
module called "Polydata to Labelmap" that may belong to plastimatch but I am
not sure it can help in any way to get contours in DICOM RT structure
format.

Thanks
Devakumar

-----Original Message-----
From: Sharp, Gregory C. [mailto:[hidden email]]
Sent: Friday, June 17, 2011 9:17 AM
To: Devakumar; [hidden email]
Subject: RE: [slicer-users] Contouring for Radiotherapy application

Hi Devakumar

At this time, it is still very difficult to create DICOM RT contours
using the Slicer editor.

For a single structure you can probably use the plastimatch DICOM-RT
export function.  You might even be able to get multiple non-overlapping
structures to work too.  If you want to try this, be sure to use structure
numbers which are a power of two: 1, 2, 4, 8, ...

Greg

________________________________

From: [hidden email] on behalf of Devakumar
Sent: Thu 6/16/2011 10:59 PM
To: [hidden email]
Subject: [slicer-users] Contouring for Radiotherapy application



Dear Slicer group

I would like to contour tumor and organs from the CT or MRI, convert
contours into DICOM RT structures and transfer to Radiotherapy reatment
planning system. The segmentation modules in Slicer are not giving contours.
Please help me.

Best regards
Devakumar


----------------------------------------------------------------------------
-------------------------
Devakumar, Ph.D., D.R.P.
Department of Nuclear Medicine
Christian Medical College
Vellore, India
Phone: +91 9994206171
----------------------------------------------------------------------------
-------------------------



_______________________________________________
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




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: Contouring for Radiotherapy application

madanrao
Hello Dr.Devakumar,

I think ModelIntoLabelVolume and Mask Image modules of Slicer3 can be used on models
in generating DICOM RT images.

I can help you build templates for EM Segmentation of brain for CLI batch building. This can
be used to standardize your DICOM RT image building.

Hope this helps.
AM Mohan Rao


On Sat, Jun 18, 2011 at 6:49 PM, Sharp, Gregory C. <[hidden email]> wrote:
Hi Devakumar,

The plastimatch modules will show up near the bottom of the
modules dropdown list.  They are all in their own "Plastimatch" group.
Within Plastimatch group should be a menu item "DICOM / DICOM-RT
Export".

If the extension installed properly, you should see the following:

(1) The extension install directory is added to the slicer module search
path.  Go to View -> Application Settings -> Module Settings, and
you will find the list of directores where modules are searched.

On Windows 7, the extension install directory looks like this:

C:/Users/gcs6/AppData/Local/Temp/Slicer3/@SVN@/plastimatch-slicer

For the @SVN@ part, you will need to replace with the Slicer svn version,
which is probably something like "16156".

(2) The extension files, such as plastimatch_slicer_dicomrt_export.exe,
are located in your extension install directory.

So I suggest to check the above items, see if everything got installed
correctly.

Greg

________________________________

From: Devakumar [mailto:[hidden email]]
Sent: Fri 6/17/2011 1:14 AM
To: Sharp, Gregory C.; [hidden email]
Subject: RE: Contouring for Radiotherapy application



Dear Greg

Thank you. I installed Slicer from the binary file
"Slicer3-3.6.4-beta-2011-06-10-win32.exe". I used extension manager to add
the plastimatch. I could not see any plastimatch modules (like DICOM RT
Import Export) in Slicer after the installation of extension. There is a
module called "Polydata to Labelmap" that may belong to plastimatch but I am
not sure it can help in any way to get contours in DICOM RT structure
format.

Thanks
Devakumar

-----Original Message-----
From: Sharp, Gregory C. [mailto:[hidden email]]
Sent: Friday, June 17, 2011 9:17 AM
To: Devakumar; [hidden email]
Subject: RE: [slicer-users] Contouring for Radiotherapy application

Hi Devakumar

At this time, it is still very difficult to create DICOM RT contours
using the Slicer editor.

For a single structure you can probably use the plastimatch DICOM-RT
export function.  You might even be able to get multiple non-overlapping
structures to work too.  If you want to try this, be sure to use structure
numbers which are a power of two: 1, 2, 4, 8, ...

Greg

________________________________

From: [hidden email] on behalf of Devakumar
Sent: Thu 6/16/2011 10:59 PM
To: [hidden email]
Subject: [slicer-users] Contouring for Radiotherapy application



Dear Slicer group

I would like to contour tumor and organs from the CT or MRI, convert
contours into DICOM RT structures and transfer to Radiotherapy reatment
planning system. The segmentation modules in Slicer are not giving contours.
Please help me.

Best regards
Devakumar


----------------------------------------------------------------------------
-------------------------
Devakumar, Ph.D., D.R.P.
Department of Nuclear Medicine
Christian Medical College
Vellore, India
Phone: +91 9994206171
----------------------------------------------------------------------------
-------------------------



_______________________________________________
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




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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