Using Plastimatch to estimate dose to organs

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Using Plastimatch to estimate dose to organs

Ganesh Narayanasamy-2

I am using Plastimatch plugin in Slicer3 3.6 in doing Bspline registration of 2 CT data sets - planning CT (pCT) and the treatment-day CT (tCT). The pCT comes with physician segmented contours which I can convert to labelmap. My goal was to use the Bspine registration parameters to get the contours on the tCT, which I could using Plastimatch's XFORMWARP feature.
Next, a sanity check. I would like to get the dose to organs in the label map (in units of cGy) in the pCT data set. This is theoretically, the planned dose so that I can compare with the treatment planning system's calculation of dose.
I would like to compute the dose to organs in the label map in the tCT data set. This is the calculation of dose
delivered to organs.
I was told that there is a way to display the dose-volume histogram in Slicer4. If so, can I still keep the current version of Slicer3 and install Slicer4, as the latter is a beta version.


Thanks a ton,
Ganesh


************************************************************************
"What the mind of man can conceive and believe, It can achieve" - Napolean Hill
-Ganesh Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer Center
************************************************************************

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Re: Using Plastimatch to estimate dose to organs

Julien Finet
Hi Ganesh,

Not sure if it answers your question, but you can safely install Slicer3 and Slicer4 at the same time, they won't interfere with each other.

Julien.

On Fri, Aug 5, 2011 at 3:37 PM, Ganesh Narayanasamy <[hidden email]> wrote:

I am using Plastimatch plugin in Slicer3 3.6 in doing Bspline registration of 2 CT data sets - planning CT (pCT) and the treatment-day CT (tCT). The pCT comes with physician segmented contours which I can convert to labelmap. My goal was to use the Bspine registration parameters to get the contours on the tCT, which I could using Plastimatch's XFORMWARP feature.
Next, a sanity check. I would like to get the dose to organs in the label map (in units of cGy) in the pCT data set. This is theoretically, the planned dose so that I can compare with the treatment planning system's calculation of dose.
I would like to compute the dose to organs in the label map in the tCT data set. This is the calculation of dose
delivered to organs.
I was told that there is a way to display the dose-volume histogram in Slicer4. If so, can I still keep the current version of Slicer3 and install Slicer4, as the latter is a beta version.


Thanks a ton,
Ganesh


************************************************************************
"What the mind of man can conceive and believe, It can achieve" - Napolean Hill
-Ganesh Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer Center
************************************************************************

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Re: Using Plastimatch to estimate dose to organs

Ganesh Narayanasamy-2

Thanks for the suggestion.. I will try installing Slicer4. I am using CERR in Matlab for calculating doses, after doing a DICOM-RT export from Plastimatch.

I have a query regarding label maps. The 2 images uploaded here have label maps. The planning CT image has clear labelmaps while the labelmaps in the deformed image has jagged or irregular boundary. These irregular boundary appears as multiple organs, which is not correct.

http://www.4shared.com/photo/oqGFH-JD/Planning_LMap.html
and
http://www.4shared.com/photo/gsIzaFsL/Deformed_LMap.html

I tried the Editor module, but not of much help. Can someone tell me how to fix the jagged edges.

Thanks,
Ganesh


From: [hidden email]
Date: Fri, 5 Aug 2011 15:59:47 -0400
Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
To: [hidden email]
CC: [hidden email]

Hi Ganesh,

Not sure if it answers your question, but you can safely install Slicer3 and Slicer4 at the same time, they won't interfere with each other.

Julien.

On Fri, Aug 5, 2011 at 3:37 PM, Ganesh Narayanasamy <[hidden email]> wrote:

I am using Plastimatch plugin in Slicer3 3.6 in doing Bspline registration of 2 CT data sets - planning CT (pCT) and the treatment-day CT (tCT). The pCT comes with physician segmented contours which I can convert to labelmap. My goal was to use the Bspine registration parameters to get the contours on the tCT, which I could using Plastimatch's XFORMWARP feature.
Next, a sanity check. I would like to get the dose to organs in the label map (in units of cGy) in the pCT data set. This is theoretically, the planned dose so that I can compare with the treatment planning system's calculation of dose.
I would like to compute the dose to organs in the label map in the tCT data set. This is the calculation of dose
delivered to organs.
I was told that there is a way to display the dose-volume histogram in Slicer4. If so, can I still keep the current version of Slicer3 and install Slicer4, as the latter is a beta version.


Thanks a ton,
Ganesh


************************************************************************
"What the mind of man can conceive and believe, It can achieve" - Napolean Hill
-Ganesh Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer Center
************************************************************************

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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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Re: Using Plastimatch to estimate dose to organs

Andras Lasso

Hi Ganesh,

 

When you transform labelmaps then you have to use nearest-neighbor interpolation (or no interpolation), then you will get correct voxel values at the boundary. Which module did you use for the transformation? Does it have an option for disabling interpolation?

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Ganesh Narayanasamy
Sent: 2011-August-05 5:06 PM
To: [hidden email]
Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs

 


Thanks for the suggestion.. I will try installing Slicer4. I am using CERR in Matlab for calculating doses, after doing a DICOM-RT export from Plastimatch.

I have a query regarding label maps. The 2 images uploaded here have label maps. The planning CT image has clear labelmaps while the labelmaps in the deformed image has jagged or irregular boundary. These irregular boundary appears as multiple organs, which is not correct.

http://www.4shared.com/photo/oqGFH-JD/Planning_LMap.html
and
http://www.4shared.com/photo/gsIzaFsL/Deformed_LMap.html

I tried the Editor module, but not of much help. Can someone tell me how to fix the jagged edges.

Thanks,
Ganesh


From: [hidden email]
Date: Fri, 5 Aug 2011 15:59:47 -0400
Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
To: [hidden email]
CC: [hidden email]

Hi Ganesh,

 

Not sure if it answers your question, but you can safely install Slicer3 and Slicer4 at the same time, they won't interfere with each other.

 

Julien.

On Fri, Aug 5, 2011 at 3:37 PM, Ganesh Narayanasamy <[hidden email]> wrote:


I am using Plastimatch plugin in Slicer3 3.6 in doing Bspline registration of 2 CT data sets - planning CT (pCT) and the treatment-day CT (tCT). The pCT comes with physician segmented contours which I can convert to labelmap. My goal was to use the Bspine registration parameters to get the contours on the tCT, which I could using Plastimatch's XFORMWARP feature.
Next, a sanity check. I would like to get the dose to organs in the label map (in units of cGy) in the pCT data set. This is theoretically, the planned dose so that I can compare with the treatment planning system's calculation of dose.
I would like to compute the dose to organs in the label map in the tCT data set. This is the calculation of dose delivered to organs.
I was told that there is a way to display the dose-volume histogram in Slicer4. If so, can I still keep the current version of Slicer3 and install Slicer4, as the latter is a beta version.


Thanks a ton,
Ganesh


************************************************************************
"What the mind of man can conceive and believe, It can achieve" - Napolean Hill
-Ganesh Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer Center
************************************************************************


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

 


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Re: Using Plastimatch to estimate dose to organs

Sharp, Gregory C.

Hi Ganesh,

Well, I guess I can explain this.  The plastimatch command line
program automatically detects if an image is a structure set,
and uses nearest-neighbor interpolation.  But I think there is no way
to do this in Slicer.

As a workaround, I added extra input / output options to XFORMwarp plugin.  
If you use the "SS volume" dropdowns, you will get nearest-neighbor
interpolation.  The new UI is in plastimatch build 2649 or better,
hopefully available tomorrow from extension manager.

Greg

-----Original Message-----
From: [hidden email] on behalf of Andras Lasso
Sent: Sun 8/7/2011 3:21 PM
To: 'Ganesh Narayanasamy'
Cc: [hidden email]
Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
 
Hi Ganesh,

 

When you transform labelmaps then you have to use nearest-neighbor
interpolation (or no interpolation), then you will get correct voxel values
at the boundary. Which module did you use for the transformation? Does it
have an option for disabling interpolation?

 

Andras

 

From: [hidden email]
[mailto:[hidden email]] On Behalf Of Ganesh
Narayanasamy
Sent: 2011-August-05 5:06 PM
To: [hidden email]
Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs

 


Thanks for the suggestion.. I will try installing Slicer4. I am using CERR
in Matlab for calculating doses, after doing a DICOM-RT export from
Plastimatch.

I have a query regarding label maps. The 2 images uploaded here have label
maps. The planning CT image has clear labelmaps while the labelmaps in the
deformed image has jagged or irregular boundary. These irregular boundary
appears as multiple organs, which is not correct.

http://www.4shared.com/photo/oqGFH-JD/Planning_LMap.html
and
http://www.4shared.com/photo/gsIzaFsL/Deformed_LMap.html

I tried the Editor module, but not of much help. Can someone tell me how to
fix the jagged edges.

Thanks,
Ganesh

  _____  

From: [hidden email]
Date: Fri, 5 Aug 2011 15:59:47 -0400
Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
To: [hidden email]
CC: [hidden email]

Hi Ganesh,

 

Not sure if it answers your question, but you can safely install Slicer3 and
Slicer4 at the same time, they won't interfere with each other.

 

Julien.

On Fri, Aug 5, 2011 at 3:37 PM, Ganesh Narayanasamy <[hidden email]>
wrote:


I am using Plastimatch plugin in Slicer3 3.6 in doing Bspline registration
of 2 CT data sets - planning CT (pCT) and the treatment-day CT (tCT). The
pCT comes with physician segmented contours which I can convert to labelmap.
My goal was to use the Bspine registration parameters to get the contours on
the tCT, which I could using Plastimatch's XFORMWARP feature.
Next, a sanity check. I would like to get the dose to organs in the label
map (in units of cGy) in the pCT data set. This is theoretically, the
planned dose so that I can compare with the treatment planning system's
calculation of dose.
I would like to compute the dose to organs in the label map in the tCT data
set. This is the calculation of dose delivered to organs.
I was told that there is a way to display the dose-volume histogram in
Slicer4. If so, can I still keep the current version of Slicer3 and install
Slicer4, as the latter is a beta version.


Thanks a ton,
Ganesh


************************************************************************
"What the mind of man can conceive and believe, It can achieve" - Napolean
Hill
-Ganesh Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer Center
************************************************************************


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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: Using Plastimatch to estimate dose to organs

Ganesh Narayanasamy-2
Thanks for making the changes.
One quick question.. how would I get to the nightly builds of Slicer 4? All I see here are Slicer 3.6.4 Beta :
http://www.slicer.org/pages/Special:SlicerDownloads

Thanks,
Ganesh


> Subject: RE: [slicer-users] Using Plastimatch to estimate dose to organs

> Date: Sun, 7 Aug 2011 21:42:22 -0400
> From: [hidden email]
> To: [hidden email]; [hidden email]
> CC: [hidden email]
>
>
> Hi Ganesh,
>
> Well, I guess I can explain this. The plastimatch command line
> program automatically detects if an image is a structure set,
> and uses nearest-neighbor interpolation. But I think there is no way
> to do this in Slicer.
>
> As a workaround, I added extra input / output options to XFORMwarp plugin.
> If you use the "SS volume" dropdowns, you will get nearest-neighbor
> interpolation. The new UI is in plastimatch build 2649 or better,
> hopefully available tomorrow from extension manager.
>
> Greg
>
> -----Original Message-----
> From: [hidden email] on behalf of Andras Lasso
> Sent: Sun 8/7/2011 3:21 PM
> To: 'Ganesh Narayanasamy'
> Cc: [hidden email]
> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
>
> Hi Ganesh,
>
>
>
> When you transform labelmaps then you have to use nearest-neighbor
> interpolation (or no interpolation), then you will get correct voxel values
> at the boundary. Which module did you use for the transformation? Does it
> have an option for disabling interpolation?
>
>
>
> Andras
>
>
>
> From: [hidden email]
> [mailto:[hidden email]] On Behalf Of Ganesh
> Narayanasamy
> Sent: 2011-August-05 5:06 PM
> To: [hidden email]
> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
>
>
>
>
> Thanks for the suggestion.. I will try installing Slicer4. I am using CERR
> in Matlab for calculating doses, after doing a DICOM-RT export from
> Plastimatch.
>
> I have a query regarding label maps. The 2 images uploaded here have label
> maps. The planning CT image has clear labelmaps while the labelmaps in the
> deformed image has jagged or irregular boundary. These irregular boundary
> appears as multiple organs, which is not correct.
>
> http://www.4shared.com/photo/oqGFH-JD/Planning_LMap.html
> and
> http://www.4shared.com/photo/gsIzaFsL/Deformed_LMap.html
>
> I tried the Editor module, but not of much help. Can someone tell me how to
> fix the jagged edges.
>
> Thanks,
> Ganesh
>
> _____
>
> From: [hidden email]
> Date: Fri, 5 Aug 2011 15:59:47 -0400
> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
> To: [hidden email]
> CC: [hidden email]
>
> Hi Ganesh,
>
>
>
> Not sure if it answers your question, but you can safely install Slicer3 and
> Slicer4 at the same time, they won't interfere with each other.
>
>
>
> Julien.
>
> On Fri, Aug 5, 2011 at 3:37 PM, Ganesh Narayanasamy <[hidden email]>
> wrote:
>
>
> I am using Plastimatch plugin in Slicer3 3.6 in doing Bspline registration
> of 2 CT data sets - planning CT (pCT) and the treatment-day CT (tCT). The
> pCT comes with physician segmented contours which I can convert to labelmap.
> My goal was to use the Bspine registration parameters to get the contours on
> the tCT, which I could using Plastimatch's XFORMWARP feature.
> Next, a sanity check. I would like to get the dose to organs in the label
> map (in units of cGy) in the pCT data set. This is theoretically, the
> planned dose so that I can compare with the treatment planning system's
> calculation of dose.
> I would like to compute the dose to organs in the label map in the tCT data
> set. This is the calculation of dose delivered to organs.
> I was told that there is a way to display the dose-volume histogram in
> Slicer4. If so, can I still keep the current version of Slicer3 and install
> Slicer4, as the latter is a beta version.
>
>
> Thanks a ton,
> Ganesh
>
>
> ************************************************************************
> "What the mind of man can conceive and believe, It can achieve" - Napolean
> Hill
> -Ganesh Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer Center
> ************************************************************************
>
>
> _______________________________________________
> 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: Using Plastimatch to estimate dose to organs

Steve Pieper
Hi Ganesh -

The nightly builds for slicer4 are here:

http://cdash.org/slicer4/index.php?project=Slicer4

When the build completes without errors, there's a small gold box icon
in the Build Name column that will get you to the downloads.

-Steve

On Wed, Aug 10, 2011 at 2:11 PM, Ganesh Narayanasamy
<[hidden email]> wrote:

> Thanks for making the changes.
> One quick question.. how would I get to the nightly builds of Slicer 4? All
> I see here are Slicer 3.6.4 Beta :
> http://www.slicer.org/pages/Special:SlicerDownloads
>
> Thanks,
> Ganesh
>
>
>> Subject: RE: [slicer-users] Using Plastimatch to estimate dose to organs
>> Date: Sun, 7 Aug 2011 21:42:22 -0400
>> From: [hidden email]
>> To: [hidden email]; [hidden email]
>> CC: [hidden email]
>>
>>
>> Hi Ganesh,
>>
>> Well, I guess I can explain this. The plastimatch command line
>> program automatically detects if an image is a structure set,
>> and uses nearest-neighbor interpolation. But I think there is no way
>> to do this in Slicer.
>>
>> As a workaround, I added extra input / output options to XFORMwarp plugin.
>> If you use the "SS volume" dropdowns, you will get nearest-neighbor
>> interpolation. The new UI is in plastimatch build 2649 or better,
>> hopefully available tomorrow from extension manager.
>>
>> Greg
>>
>> -----Original Message-----
>> From: [hidden email] on behalf of Andras Lasso
>> Sent: Sun 8/7/2011 3:21 PM
>> To: 'Ganesh Narayanasamy'
>> Cc: [hidden email]
>> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
>>
>> Hi Ganesh,
>>
>>
>>
>> When you transform labelmaps then you have to use nearest-neighbor
>> interpolation (or no interpolation), then you will get correct voxel
>> values
>> at the boundary. Which module did you use for the transformation? Does it
>> have an option for disabling interpolation?
>>
>>
>>
>> Andras
>>
>>
>>
>> From: [hidden email]
>> [mailto:[hidden email]] On Behalf Of Ganesh
>> Narayanasamy
>> Sent: 2011-August-05 5:06 PM
>> To: [hidden email]
>> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
>>
>>
>>
>>
>> Thanks for the suggestion.. I will try installing Slicer4. I am using CERR
>> in Matlab for calculating doses, after doing a DICOM-RT export from
>> Plastimatch.
>>
>> I have a query regarding label maps. The 2 images uploaded here have label
>> maps. The planning CT image has clear labelmaps while the labelmaps in the
>> deformed image has jagged or irregular boundary. These irregular boundary
>> appears as multiple organs, which is not correct.
>>
>> http://www.4shared.com/photo/oqGFH-JD/Planning_LMap.html
>> and
>> http://www.4shared.com/photo/gsIzaFsL/Deformed_LMap.html
>>
>> I tried the Editor module, but not of much help. Can someone tell me how
>> to
>> fix the jagged edges.
>>
>> Thanks,
>> Ganesh
>>
>> _____
>>
>> From: [hidden email]
>> Date: Fri, 5 Aug 2011 15:59:47 -0400
>> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
>> To: [hidden email]
>> CC: [hidden email]
>>
>> Hi Ganesh,
>>
>>
>>
>> Not sure if it answers your question, but you can safely install Slicer3
>> and
>> Slicer4 at the same time, they won't interfere with each other.
>>
>>
>>
>> Julien.
>>
>> On Fri, Aug 5, 2011 at 3:37 PM, Ganesh Narayanasamy
>> <[hidden email]>
>> wrote:
>>
>>
>> I am using Plastimatch plugin in Slicer3 3.6 in doing Bspline registration
>> of 2 CT data sets - planning CT (pCT) and the treatment-day CT (tCT). The
>> pCT comes with physician segmented contours which I can convert to
>> labelmap.
>> My goal was to use the Bspine registration parameters to get the contours
>> on
>> the tCT, which I could using Plastimatch's XFORMWARP feature.
>> Next, a sanity check. I would like to get the dose to organs in the label
>> map (in units of cGy) in the pCT data set. This is theoretically, the
>> planned dose so that I can compare with the treatment planning system's
>> calculation of dose.
>> I would like to compute the dose to organs in the label map in the tCT
>> data
>> set. This is the calculation of dose delivered to organs.
>> I was told that there is a way to display the dose-volume histogram in
>> Slicer4. If so, can I still keep the current version of Slicer3 and
>> install
>> Slicer4, as the latter is a beta version.
>>
>>
>> Thanks a ton,
>> Ganesh
>>
>>
>> ************************************************************************
>> "What the mind of man can conceive and believe, It can achieve" - Napolean
>> Hill
>> -Ganesh Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer Center
>> ************************************************************************
>>
>>
>> _______________________________________________
>> 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.
>>
>
> _______________________________________________
> 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: Using Plastimatch to estimate dose to organs

Ganesh Narayanasamy-2
In reply to this post by Sharp, Gregory C.

In the Nightly build that I downloaded today, I cannot find any extensions in the Extension Manager which is strange. It is quite possible that I have messed up something here.. can you help me find the extensions in  Slicer3-3.6.4-beta-2011-08-12-win32.exe

FYI, in the "where to search" drop-down menu, "http://ext.slicer.org/ext/trunk/16811-win32" is displayed.

Thanks,
Ganesh

> Subject: RE: [slicer-users] Using Plastimatch to estimate dose to organs

> Date: Sun, 7 Aug 2011 21:42:22 -0400
> From: [hidden email]
> To: [hidden email]; [hidden email]
> CC: [hidden email]
>
>
> Hi Ganesh,
>
> Well, I guess I can explain this. The plastimatch command line
> program automatically detects if an image is a structure set,
> and uses nearest-neighbor interpolation. But I think there is no way
> to do this in Slicer.
>
> As a workaround, I added extra input / output options to XFORMwarp plugin.
> If you use the "SS volume" dropdowns, you will get nearest-neighbor
> interpolation. The new UI is in plastimatch build 2649 or better,
> hopefully available tomorrow from extension manager.
>
> Greg
>
> -----Original Message-----
> From: [hidden email] on behalf of Andras Lasso
> Sent: Sun 8/7/2011 3:21 PM
> To: 'Ganesh Narayanasamy'
> Cc: [hidden email]
> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
>
> Hi Ganesh,
>
>
>
> When you transform labelmaps then you have to use nearest-neighbor
> interpolation (or no interpolation), then you will get correct voxel values
> at the boundary. Which module did you use for the transformation? Does it
> have an option for disabling interpolation?
>
>
>
> Andras
>
>
>
> From: [hidden email]
> [mailto:[hidden email]] On Behalf Of Ganesh
> Narayanasamy
> Sent: 2011-August-05 5:06 PM
> To: [hidden email]
> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
>
>
>
>
> Thanks for the suggestion.. I will try installing Slicer4. I am using CERR
> in Matlab for calculating doses, after doing a DICOM-RT export from
> Plastimatch.
>
> I have a query regarding label maps. The 2 images uploaded here have label
> maps. The planning CT image has clear labelmaps while the labelmaps in the
> deformed image has jagged or irregular boundary. These irregular boundary
> appears as multiple organs, which is not correct.
>
> http://www.4shared.com/photo/oqGFH-JD/Planning_LMap.html
> and
> http://www.4shared.com/photo/gsIzaFsL/Deformed_LMap.html
>
> I tried the Editor module, but not of much help. Can someone tell me how to
> fix the jagged edges.
>
> Thanks,
> Ganesh
>
> _____
>
> From: [hidden email]
> Date: Fri, 5 Aug 2011 15:59:47 -0400
> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
> To: [hidden email]
> CC: [hidden email]
>
> Hi Ganesh,
>
>
>
> Not sure if it answers your question, but you can safely install Slicer3 and
> Slicer4 at the same time, they won't interfere with each other.
>
>
>
> Julien.
>
> On Fri, Aug 5, 2011 at 3:37 PM, Ganesh Narayanasamy <[hidden email]>
> wrote:
>
>
> I am using Plastimatch plugin in Slicer3 3.6 in doing Bspline registration
> of 2 CT data sets - planning CT (pCT) and the treatment-day CT (tCT). The
> pCT comes with physician segmented contours which I can convert to labelmap.
> My goal was to use the Bspine registration parameters to get the contours on
> the tCT, which I could using Plastimatch's XFORMWARP feature.
> Next, a sanity check. I would like to get the dose to organs in the label
> map (in units of cGy) in the pCT data set. This is theoretically, the
> planned dose so that I can compare with the treatment planning system's
> calculation of dose.
> I would like to compute the dose to organs in the label map in the tCT data
> set. This is the calculation of dose delivered to organs.
> I was told that there is a way to display the dose-volume histogram in
> Slicer4. If so, can I still keep the current version of Slicer3 and install
> Slicer4, as the latter is a beta version.
>
>
> Thanks a ton,
> Ganesh
>
>
> ************************************************************************
> "What the mind of man can conceive and believe, It can achieve" - Napolean
> Hill
> -Ganesh Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer Center
> ************************************************************************
>
>
> _______________________________________________
> 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: Using Plastimatch to estimate dose to organs

Dominique Belhachemi
On Fri, Aug 12, 2011 at 2:56 PM, Ganesh Narayanasamy
<[hidden email]> wrote:
>
> In the Nightly build that I downloaded today, I cannot find any extensions
> in the Extension Manager which is strange. It is quite possible that I have
> messed up something here.. can you help me find the extensions in
> Slicer3-3.6.4-beta-2011-08-12-win32.exe
>
> FYI, in the "where to search" drop-down menu,
> "http://ext.slicer.org/ext/trunk/16811-win32" is displayed.
>
Please change it to an older version (Aug 8th)
http://ext.slicer.org/ext/trunk/16799-win32/

Dominique
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Re: Using Plastimatch to estimate dose to organs

Steve Pieper
Thanks for the heads up about the server - it's repopulating now with
the latest extension builds and should be up to date with in the next
hour or so.

-Steve

On Fri, Aug 12, 2011 at 3:12 PM, Dominique Belhachemi
<[hidden email]> wrote:

> On Fri, Aug 12, 2011 at 2:56 PM, Ganesh Narayanasamy
> <[hidden email]> wrote:
>>
>> In the Nightly build that I downloaded today, I cannot find any extensions
>> in the Extension Manager which is strange. It is quite possible that I have
>> messed up something here.. can you help me find the extensions in
>> Slicer3-3.6.4-beta-2011-08-12-win32.exe
>>
>> FYI, in the "where to search" drop-down menu,
>> "http://ext.slicer.org/ext/trunk/16811-win32" is displayed.
>>
> Please change it to an older version (Aug 8th)
> http://ext.slicer.org/ext/trunk/16799-win32/
>
> Dominique
> _______________________________________________
> 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: Using Plastimatch to estimate dose to organs

Ganesh Narayanasamy-2

In our institution we use the CMS-XiO treatment planning system for radiation therapy. One of the requirements in XiO is that each planning CT slice should have a patient contour and this is absolutely necessary before we can even place the beams.
However, Plastimatch does not let me import DICOM-RT plans with over-lapping contours. This in effect means, once we have the patient contour (as needed by XiO), we cannot have anything inside the patient contour - be it tumor volume or organs at risk. Needless to say, if I cannot have any of these organ contours, I cannot calculate dose to any organ.
This is a catch-22 situation. Can someone bail me out?

Thanks,
Ganesh

> Date: Fri, 12 Aug 2011 15:54:03 -0400

> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
> From: [hidden email]
> To: [hidden email]
> CC: [hidden email]; [hidden email]
>
> Thanks for the heads up about the server - it's repopulating now with
> the latest extension builds and should be up to date with in the next
> hour or so.
>
> -Steve
>
> On Fri, Aug 12, 2011 at 3:12 PM, Dominique Belhachemi
> <[hidden email]> wrote:
> > On Fri, Aug 12, 2011 at 2:56 PM, Ganesh Narayanasamy
> > <[hidden email]> wrote:
> >>
> >> In the Nightly build that I downloaded today, I cannot find any extensions
> >> in the Extension Manager which is strange. It is quite possible that I have
> >> messed up something here.. can you help me find the extensions in
> >> Slicer3-3.6.4-beta-2011-08-12-win32.exe
> >>
> >> FYI, in the "where to search" drop-down menu,
> >> "http://ext.slicer.org/ext/trunk/16811-win32" is displayed.
> >>
> > Please change it to an older version (Aug 8th)
> > http://ext.slicer.org/ext/trunk/16799-win32/
> >
> > Dominique
> > _______________________________________________
> > 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: Using Plastimatch to estimate dose to organs

Sharp, Gregory C.

Hi Ganesh,

The "ss image" does allow overlapping structures.  However,
in the plugin you are limited to 32 structures, and you can't
(easily) edit them, and the structure names get lost.

As a result, I can't recommend using Slicer for DVH analysis
at this time.  Maybe you could try the plastimatch command line
tools instead?

Greg

-----Original Message-----
From: [hidden email] on behalf of Ganesh Narayanasamy
Sent: Sat 8/13/2011 9:59 AM
To: [hidden email]
Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
 


In our institution we use the CMS-XiO treatment planning system for radiation
therapy. One of the requirements in XiO is that each planning CT slice should
have a patient contour and this is absolutely necessary before we can even place
the beams.
However, Plastimatch does not let me import DICOM-RT plans with over-lapping
contours. This in effect means, once we have the patient contour (as needed by
XiO), we cannot have anything inside the patient contour - be it tumor volume or
organs at risk. Needless to say, if I cannot have any of these organ contours, I
cannot calculate dose to any organ.
This is a catch-22 situation. Can someone bail me out?

Thanks,
Ganesh

> Date: Fri, 12 Aug 2011 15:54:03 -0400
> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
> From: [hidden email]
> To: [hidden email]
> CC: [hidden email]; [hidden email]
>
> Thanks for the heads up about the server - it's repopulating now with
> the latest extension builds and should be up to date with in the next
> hour or so.
>
> -Steve
>
> On Fri, Aug 12, 2011 at 3:12 PM, Dominique Belhachemi
> <[hidden email]> wrote:
> > On Fri, Aug 12, 2011 at 2:56 PM, Ganesh Narayanasamy
> > <[hidden email]> wrote:
> >>
> >> In the Nightly build that I downloaded today, I cannot find any extensions
> >> in the Extension Manager which is strange. It is quite possible that I have
> >> messed up something here.. can you help me find the extensions in
> >> Slicer3-3.6.4-beta-2011-08-12-win32.exe
> >>
> >> FYI, in the "where to search" drop-down menu,
> >> "http://ext.slicer.org/ext/trunk/16811-win32" is displayed.
> >>
> > Please change it to an older version (Aug 8th)
> > http://ext.slicer.org/ext/trunk/16799-win32/
> >
> > Dominique
> > _______________________________________________
> > 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: Using Plastimatch to estimate dose to organs

Ganesh Narayanasamy-2

Sure Greg. I went through the instructions in http://plastimatch.org/contents.html. Can you point me to the deformation of two 3D CT/MRI images of the same patient acquired at different times; applying the deformation to organs; DVH comparison of organs before and after deformation; generation of 3D deformation grid or displacement vector map.

In the meantime, let me try using "ss image" in the XFORM Warping transform module in Plastimatch from Slicer3D. If I can process overlapping structures, that is really ideal. Do you know of a way to maintain all the structures in a particular order so that we can keep tab on them even when the names get lost?

Appreciate your help as always,
Ganesh


> Subject: RE: [slicer-users] Using Plastimatch to estimate dose to organs

> Date: Sat, 13 Aug 2011 12:17:03 -0400
> From: [hidden email]
> To: [hidden email]; [hidden email]
>
>
> Hi Ganesh,
>
> The "ss image" does allow overlapping structures. However,
> in the plugin you are limited to 32 structures, and you can't
> (easily) edit them, and the structure names get lost.
>
> As a result, I can't recommend using Slicer for DVH analysis
> at this time. Maybe you could try the plastimatch command line
> tools instead?
>
> Greg
>
> -----Original Message-----
> From: [hidden email] on behalf of Ganesh Narayanasamy
> Sent: Sat 8/13/2011 9:59 AM
> To: [hidden email]
> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
>
>
>
> In our institution we use the CMS-XiO treatment planning system for radiation
> therapy. One of the requirements in XiO is that each planning CT slice should
> have a patient contour and this is absolutely necessary before we can even place
> the beams.
> However, Plastimatch does not let me import DICOM-RT plans with over-lapping
> contours. This in effect means, once we have the patient contour (as needed by
> XiO), we cannot have anything inside the patient contour - be it tumor volume or
> organs at risk. Needless to say, if I cannot have any of these organ contours, I
> cannot calculate dose to any organ.
> This is a catch-22 situation. Can someone bail me out?
>
> Thanks,
> Ganesh
>
> > Date: Fri, 12 Aug 2011 15:54:03 -0400
> > Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
> > From: [hidden email]
> > To: [hidden email]
> > CC: [hidden email]; [hidden email]
> >
> > Thanks for the heads up about the server - it's repopulating now with
> > the latest extension builds and should be up to date with in the next
> > hour or so.
> >
> > -Steve
> >
> > On Fri, Aug 12, 2011 at 3:12 PM, Dominique Belhachemi
> > <[hidden email]> wrote:
> > > On Fri, Aug 12, 2011 at 2:56 PM, Ganesh Narayanasamy
> > > <[hidden email]> wrote:
> > >>
> > >> In the Nightly build that I downloaded today, I cannot find any extensions
> > >> in the Extension Manager which is strange. It is quite possible that I have
> > >> messed up something here.. can you help me find the extensions in
> > >> Slicer3-3.6.4-beta-2011-08-12-win32.exe
> > >>
> > >> FYI, in the "where to search" drop-down menu,
> > >> "http://ext.slicer.org/ext/trunk/16811-win32" is displayed.
> > >>
> > > Please change it to an older version (Aug 8th)
> > > http://ext.slicer.org/ext/trunk/16799-win32/
> > >
> > > Dominique
> > > _______________________________________________
> > > 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.
>

_______________________________________________
slicer-users mailing list
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Re: Using Plastimatch to estimate dose to organs

Sharp, Gregory C.

Hi Ganesh,

I made an update to the DICOM RT import/export plugins.

Now you have an option to save the names of the structures
into a separate text file when you import.

Then, when you export, you can load that text file, and
the structures will have the correct names in DICOM RT.

As described before, you need to import/warp/export the
"SS image", not the "labelmap image".

Could you please test this new version?  The patch is included
in plastimatch version 2674 or greater.  If all goes well,
it will get compiled by the build machines tonight.

Greg

-----Original Message-----
From: [hidden email] on behalf of Ganesh Narayanasamy
Sent: Sat 8/13/2011 1:20 PM
To: [hidden email]
Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
 


Sure Greg. I went through the instructions in
http://plastimatch.org/contents.html. Can you point me to the deformation of two
3D CT/MRI images of the same patient acquired at different times; applying the
deformation to organs; DVH comparison of organs before and after deformation;
generation of 3D deformation grid or displacement vector map.

In the meantime, let me try using "ss image" in the XFORM Warping transform
module in Plastimatch from Slicer3D. If I can process overlapping structures,
that is really ideal. Do you know of a way to maintain all the structures in a
particular order so that we can keep tab on them even when the names get lost?

Appreciate your help as always,
Ganesh


> Subject: RE: [slicer-users] Using Plastimatch to estimate dose to organs
> Date: Sat, 13 Aug 2011 12:17:03 -0400
> From: [hidden email]
> To: [hidden email]; [hidden email]
>
>
> Hi Ganesh,
>
> The "ss image" does allow overlapping structures.  However,
> in the plugin you are limited to 32 structures, and you can't
> (easily) edit them, and the structure names get lost.
>
> As a result, I can't recommend using Slicer for DVH analysis
> at this time.  Maybe you could try the plastimatch command line
> tools instead?
>
> Greg
>
> -----Original Message-----
> From: [hidden email] on behalf of Ganesh Narayanasamy
> Sent: Sat 8/13/2011 9:59 AM
> To: [hidden email]
> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
>  
>
>
> In our institution we use the CMS-XiO treatment planning system for radiation
> therapy. One of the requirements in XiO is that each planning CT slice should
> have a patient contour and this is absolutely necessary before we can even
place
> the beams.
> However, Plastimatch does not let me import DICOM-RT plans with over-lapping
> contours. This in effect means, once we have the patient contour (as needed by
> XiO), we cannot have anything inside the patient contour - be it tumor volume
or
> organs at risk. Needless to say, if I cannot have any of these organ contours,
I

> cannot calculate dose to any organ.
> This is a catch-22 situation. Can someone bail me out?
>
> Thanks,
> Ganesh
>
> > Date: Fri, 12 Aug 2011 15:54:03 -0400
> > Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
> > From: [hidden email]
> > To: [hidden email]
> > CC: [hidden email]; [hidden email]
> >
> > Thanks for the heads up about the server - it's repopulating now with
> > the latest extension builds and should be up to date with in the next
> > hour or so.
> >
> > -Steve
> >
> > On Fri, Aug 12, 2011 at 3:12 PM, Dominique Belhachemi
> > <[hidden email]> wrote:
> > > On Fri, Aug 12, 2011 at 2:56 PM, Ganesh Narayanasamy
> > > <[hidden email]> wrote:
> > >>
> > >> In the Nightly build that I downloaded today, I cannot find any
extensions
> > >> in the Extension Manager which is strange. It is quite possible that I
have

> > >> messed up something here.. can you help me find the extensions in
> > >> Slicer3-3.6.4-beta-2011-08-12-win32.exe
> > >>
> > >> FYI, in the "where to search" drop-down menu,
> > >> "http://ext.slicer.org/ext/trunk/16811-win32" is displayed.
> > >>
> > > Please change it to an older version (Aug 8th)
> > > http://ext.slicer.org/ext/trunk/16799-win32/
> > >
> > > Dominique
> > > _______________________________________________
> > > 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: Using Plastimatch to estimate dose to organs

Ganesh Narayanasamy-2
In reply to this post by Ganesh Narayanasamy-2
I could not find the latest Nightly build after Slicer 3 3.6.4-beta-2011-08-12-win32.exe
I will wait for it to appear tomorrow.

-Ganesh

>

> Message: 5
> Date: Sun, 14 Aug 2011 17:12:43 -0400
> From: "Sharp, Gregory C." <[hidden email]>
> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to
> organs
> To: <[hidden email]>
> Message-ID:
> <[hidden email]>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Hi Ganesh,
>
> I made an update to the DICOM RT import/export plugins.
>
> Now you have an option to save the names of the structures
> into a separate text file when you import.
>
> Then, when you export, you can load that text file, and
> the structures will have the correct names in DICOM RT.
>
> As described before, you need to import/warp/export the
> "SS image", not the "labelmap image".
>
> Could you please test this new version? The patch is included
> in plastimatch version 2674 or greater. If all goes well,
> it will get compiled by the build machines tonight.
>
> Greg
>


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Re: Using Plastimatch to estimate dose to organs

Steve Pieper
Looks like the packaging configuration needed some updates to keep up
with the new cmake/tcl library versions - hopefully will be back in
business by tomorrow.

-Steve

On Mon, Aug 15, 2011 at 2:20 PM, Ganesh Narayanasamy
<[hidden email]> wrote:

> I could not find the latest Nightly build after Slicer 3
> 3.6.4-beta-2011-08-12-win32.exe
> I will wait for it to appear tomorrow.
>
> -Ganesh
>
>>
>> Message: 5
>> Date: Sun, 14 Aug 2011 17:12:43 -0400
>> From: "Sharp, Gregory C." <[hidden email]>
>> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to
>> organs
>> To: <[hidden email]>
>> Message-ID:
>> <[hidden email]>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>>
>> Hi Ganesh,
>>
>> I made an update to the DICOM RT import/export plugins.
>>
>> Now you have an option to save the names of the structures
>> into a separate text file when you import.
>>
>> Then, when you export, you can load that text file, and
>> the structures will have the correct names in DICOM RT.
>>
>> As described before, you need to import/warp/export the
>> "SS image", not the "labelmap image".
>>
>> Could you please test this new version? The patch is included
>> in plastimatch version 2674 or greater. If all goes well,
>> it will get compiled by the build machines tonight.
>>
>> Greg
>>
>
>
> _______________________________________________
> 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: Using Plastimatch to estimate dose to organs

Ganesh Narayanasamy-2

I can see the latest Nightly build now. However the Extension Manager is not loading any extensions. I changed the link in it from
http://ext.slicer.org/ext/trunk/16821-win32
into
http://ext.slicer.org/ext/trunk/16811-win32
But it contains Plastimatch svn 2661. Greg, does it have the latest stuff that you have mentioned in your earlier email.

Thanks,
Ganesh



> Date: Mon, 15 Aug 2011 16:17:12 -0400

> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
> From: [hidden email]
> To: [hidden email]
> CC: [hidden email]
>
> Looks like the packaging configuration needed some updates to keep up
> with the new cmake/tcl library versions - hopefully will be back in
> business by tomorrow.
>
> -Steve
>
> On Mon, Aug 15, 2011 at 2:20 PM, Ganesh Narayanasamy
> <[hidden email]> wrote:
> > I could not find the latest Nightly build after Slicer 3
> > 3.6.4-beta-2011-08-12-win32.exe
> > I will wait for it to appear tomorrow.
> >
> > -Ganesh
> >
> >>
> >> Message: 5
> >> Date: Sun, 14 Aug 2011 17:12:43 -0400
> >> From: "Sharp, Gregory C." <[hidden email]>
> >> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to
> >> organs
> >> To: <[hidden email]>
> >> Message-ID:
> >> <[hidden email]>
> >> Content-Type: text/plain; charset="iso-8859-1"
> >>
> >>
> >> Hi Ganesh,
> >>
> >> I made an update to the DICOM RT import/export plugins.
> >>
> >> Now you have an option to save the names of the structures
> >> into a separate text file when you import.
> >>
> >> Then, when you export, you can load that text file, and
> >> the structures will have the correct names in DICOM RT.
> >>
> >> As described before, you need to import/warp/export the
> >> "SS image", not the "labelmap image".
> >>
> >> Could you please test this new version? The patch is included
> >> in plastimatch version 2674 or greater. If all goes well,
> >> it will get compiled by the build machines tonight.
> >>
> >> Greg
> >>
> >
> >
> > _______________________________________________
> > 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: Using Plastimatch to estimate dose to organs

Sharp, Gregory C.
Hi Ganesh,
 
No, that one won't work.  The extensions stopped building Aug 12.  
 
Greg


From: [hidden email] [mailto:[hidden email]] On Behalf Of Ganesh Narayanasamy
Sent: Tuesday, August 16, 2011 10:17 AM
To: [hidden email]
Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs


I can see the latest Nightly build now. However the Extension Manager is not loading any extensions. I changed the link in it from
http://ext.slicer.org/ext/trunk/16821-win32
into
http://ext.slicer.org/ext/trunk/16811-win32
But it contains Plastimatch svn 2661. Greg, does it have the latest stuff that you have mentioned in your earlier email.

Thanks,
Ganesh



> Date: Mon, 15 Aug 2011 16:17:12 -0400

> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
> From: [hidden email]
> To: [hidden email]
> CC: [hidden email]
>
> Looks like the packaging configuration needed some updates to keep up
> with the new cmake/tcl library versions - hopefully will be back in
> business by tomorrow.
>
> -Steve
>
> On Mon, Aug 15, 2011 at 2:20 PM, Ganesh Narayanasamy
> <[hidden email]> wrote:
> > I could not find the latest Nightly build after Slicer 3
> > 3.6.4-beta-2011-08-12-win32.exe
> > I will wait for it to appear tomorrow.
> >
> > -Ganesh
> >
> >>
> >> Message: 5
> >> Date: Sun, 14 Aug 2011 17:12:43 -0400
> >> From: "Sharp, Gregory C." <[hidden email]>
> >> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to
> >> organs
> >> To: <[hidden email]>
> >> Message-ID:
> >> <[hidden email]>
> >> Content-Type: text/plain; charset="iso-8859-1"
> >>
> >>
> >> Hi Ganesh,
> >>
> >> I made an update to the DICOM RT import/export plugins.
> >>
> >> Now you have an option to save the names of the structures
> >> into a separate text file when you import.
> >>
> >> Then, when you export, you can load that text file, and
> >> the structures will have the correct names in DICOM RT.
> >>
> >> As described before, you need to import/warp/export the
> >> "SS image", not the "labelmap image".
> >>
> >> Could you please test this new version? The patch is included
> >> in plastimatch version 2674 or greater. If all goes well,
> >> it will get compiled by the build machines tonight.
> >>
> >> Greg
> >>
> >
> >
> > _______________________________________________
> > 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]
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: Using Plastimatch to estimate dose to organs

Ganesh Narayanasamy-2

I know I am being sloppy here.. does anyone know if the latest Nightly build (2011-08-17 for win32) has all the extensions (especially Plastimatch) built in it.

Thanks,
Ganesh


Subject: RE: [slicer-users] Using Plastimatch to estimate dose to organs
Date: Tue, 16 Aug 2011 10:21:53 -0400
From: [hidden email]
To: [hidden email]; [hidden email]

Hi Ganesh,
 
No, that one won't work.  The extensions stopped building Aug 12.  
 
Greg


From: [hidden email] [mailto:[hidden email]] On Behalf Of Ganesh Narayanasamy
Sent: Tuesday, August 16, 2011 10:17 AM
To: [hidden email]
Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs


I can see the latest Nightly build now. However the Extension Manager is not loading any extensions. I changed the link in it from
http://ext.slicer.org/ext/trunk/16821-win32
into
http://ext.slicer.org/ext/trunk/16811-win32
But it contains Plastimatch svn 2661. Greg, does it have the latest stuff that you have mentioned in your earlier email.

Thanks,
Ganesh



> Date: Mon, 15 Aug 2011 16:17:12 -0400

> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
> From: [hidden email]
> To: [hidden email]
> CC: [hidden email]
>
> Looks like the packaging configuration needed some updates to keep up
> with the new cmake/tcl library versions - hopefully will be back in
> business by tomorrow.
>
> -Steve
>
> On Mon, Aug 15, 2011 at 2:20 PM, Ganesh Narayanasamy
> <[hidden email]> wrote:
> > I could not find the latest Nightly build after Slicer 3
> > 3.6.4-beta-2011-08-12-win32.exe
> > I will wait for it to appear tomorrow.
> >
> > -Ganesh
> >
> >>
> >> Message: 5
> >> Date: Sun, 14 Aug 2011 17:12:43 -0400
> >> From: "Sharp, Gregory C." <[hidden email]>
> >> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to
> >> organs
> >> To: <[hidden email]>
> >> Message-ID:
> >> <[hidden email]>
> >> Content-Type: text/plain; charset="iso-8859-1"
> >>
> >>
> >> Hi Ganesh,
> >>
> >> I made an update to the DICOM RT import/export plugins.
> >>
> >> Now you have an option to save the names of the structures
> >> into a separate text file when you import.
> >>
> >> Then, when you export, you can load that text file, and
> >> the structures will have the correct names in DICOM RT.
> >>
> >> As described before, you need to import/warp/export the
> >> "SS image", not the "labelmap image".
> >>
> >> Could you please test this new version? The patch is included
> >> in plastimatch version 2674 or greater. If all goes well,
> >> it will get compiled by the build machines tonight.
> >>
> >> Greg
> >>
> >
> >
> > _______________________________________________
> > 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: Using Plastimatch to estimate dose to organs

Steve Pieper
Hi Ganesh -

The extensions for the latest builds are back on line - plastimatch is
there for windows and other platforms, but I haven't tried it myself:

http://ext.slicer.org/ext/trunk/16821-win32/

Best,
Steve

On Wed, Aug 17, 2011 at 10:00 AM, Ganesh Narayanasamy
<[hidden email]> wrote:

>
> I know I am being sloppy here.. does anyone know if the latest Nightly build
> (2011-08-17 for win32) has all the extensions (especially Plastimatch) built
> in it.
>
> Thanks,
> Ganesh
>
> ________________________________
> Subject: RE: [slicer-users] Using Plastimatch to estimate dose to organs
> Date: Tue, 16 Aug 2011 10:21:53 -0400
> From: [hidden email]
> To: [hidden email]; [hidden email]
>
> Hi Ganesh,
>
> No, that one won't work.  The extensions stopped building Aug 12.
>
> Greg
> ________________________________
> From: [hidden email]
> [mailto:[hidden email]] On Behalf Of Ganesh
> Narayanasamy
> Sent: Tuesday, August 16, 2011 10:17 AM
> To: [hidden email]
> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
>
>
> I can see the latest Nightly build now. However the Extension Manager is not
> loading any extensions. I changed the link in it from
> http://ext.slicer.org/ext/trunk/16821-win32
> into
> http://ext.slicer.org/ext/trunk/16811-win32
> But it contains Plastimatch svn 2661. Greg, does it have the latest stuff
> that you have mentioned in your earlier email.
>
> Thanks,
> Ganesh
>
>
>
>> Date: Mon, 15 Aug 2011 16:17:12 -0400
>> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to organs
>> From: [hidden email]
>> To: [hidden email]
>> CC: [hidden email]
>>
>> Looks like the packaging configuration needed some updates to keep up
>> with the new cmake/tcl library versions - hopefully will be back in
>> business by tomorrow.
>>
>> -Steve
>>
>> On Mon, Aug 15, 2011 at 2:20 PM, Ganesh Narayanasamy
>> <[hidden email]> wrote:
>> > I could not find the latest Nightly build after Slicer 3
>> > 3.6.4-beta-2011-08-12-win32.exe
>> > I will wait for it to appear tomorrow.
>> >
>> > -Ganesh
>> >
>> >>
>> >> Message: 5
>> >> Date: Sun, 14 Aug 2011 17:12:43 -0400
>> >> From: "Sharp, Gregory C." <[hidden email]>
>> >> Subject: Re: [slicer-users] Using Plastimatch to estimate dose to
>> >> organs
>> >> To: <[hidden email]>
>> >> Message-ID:
>> >> <[hidden email]>
>> >> Content-Type: text/plain; charset="iso-8859-1"
>> >>
>> >>
>> >> Hi Ganesh,
>> >>
>> >> I made an update to the DICOM RT import/export plugins.
>> >>
>> >> Now you have an option to save the names of the structures
>> >> into a separate text file when you import.
>> >>
>> >> Then, when you export, you can load that text file, and
>> >> the structures will have the correct names in DICOM RT.
>> >>
>> >> As described before, you need to import/warp/export the
>> >> "SS image", not the "labelmap image".
>> >>
>> >> Could you please test this new version? The patch is included
>> >> in plastimatch version 2674 or greater. If all goes well,
>> >> it will get compiled by the build machines tonight.
>> >>
>> >> Greg
>> >>
>> >
>> >
>> > _______________________________________________
>> > 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.
> _______________________________________________
> 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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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
12