brain mask / dti tutorial

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brain mask / dti tutorial

Luca Fumagalli
Good morning,

I am having some problems regarding the creation of a brain mask before estimating the tensor.

I am using 3DSlicer 4.5.0-1. I followed the instructions in DiffusionMRIanalysisTutorial, but when I had to create the brain mask, I noticed that instead of "Baseline B-value threshold parameter", there was "Otsu omega threshold parameter". I tried to run the "apply" command after setting the otsu omega parameter to 0, 0.1, 0.5 (default) and 1. Every time, the result is "Status: completed with errors" and the mask doesn't appear.

Please let me know if you could help me with this impasse.

Regards,

Luca

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Re: brain mask / dti tutorial

inorton
Hello,

The algorithm has been updated to compute several threshold levels to find the ideal separation automatically. So far the changes have worked well with all of the data we have tested.

The new parameter is, as described, the maximum B-value to consider as a baseline. Some scans have non-zero (e.g. 5) B-value baseline images. In the previous version of the module, these were incorrectly excluded from the baseline generation, leading to mask generation failures -- if there are no baseline images detected, then the mask cannot be extracted.  That may be what happens when you set 0/0.5/1.  The default 100 should work fine, but adjust if necessary based on your scanning parameters.

If the above suggestion does not help, please send the error messages ("View" menu -> "Error Log"), and find out whether you can share a *anonymized* version of a typical dataset for us to investigate.

Best,
Isaiah

On Mon, Jul 25, 2016 at 11:45 AM, Luca Fumagalli <[hidden email]> wrote:
Good morning,

I am having some problems regarding the creation of a brain mask before estimating the tensor.

I am using 3DSlicer 4.5.0-1. I followed the instructions in DiffusionMRIanalysisTutorial, but when I had to create the brain mask, I noticed that instead of "Baseline B-value threshold parameter", there was "Otsu omega threshold parameter". I tried to run the "apply" command after setting the otsu omega parameter to 0, 0.1, 0.5 (default) and 1. Every time, the result is "Status: completed with errors" and the mask doesn't appear.

Please let me know if you could help me with this impasse.

Regards,

Luca

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


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Re: brain mask / dti tutorial

inorton
In reply to this post by Luca Fumagalli
Ah, my mistake for not reading closely enough. You are using the last release version, so this does not contain the updated module. In this case, the problem is exactly that the module cannot identify any baseline images. I would suggest to try the Slicer nightly, which does have the module updates including the "Baseline B-value Threshold Parameter" selector option.

(also, please cc: the mailing list in reply, so that the discussion can be recorded for others to benefit)

Best,
Isaiah

On Mon, Jul 25, 2016 at 12:27 PM, Luca Fumagalli <[hidden email]> wrote:
Thank you for your answer. The problem is that I cannot set the B-value, since the only command shown is "otsu omega threshold parameter", that goes from 0 to 1 (thus I cannot set 100).

The error log states:

Diffusion Weighted Volume Masking standard error:


C:/Program Files/Slicer 4.5.0-1/lib/Slicer-4.5/cli-modules/DiffusionWeightedVolumeMasking.exe: Error parsing Diffusion information, no B0 images


Diffusion Weighted Volume Masking completed with errors



Here is a screenshot: as you can see, there is Otsu omega threshold parameter (0.0-1.0) instead of B-value (0-100).

Immagine incorporata 1

Regards,

Luca

2016-07-25 11:58 GMT-04:00 Isaiah Norton <[hidden email]>:
Hello,

The algorithm has been updated to compute several threshold levels to find the ideal separation automatically. So far the changes have worked well with all of the data we have tested.

The new parameter is, as described, the maximum B-value to consider as a baseline. Some scans have non-zero (e.g. 5) B-value baseline images. In the previous version of the module, these were incorrectly excluded from the baseline generation, leading to mask generation failures -- if there are no baseline images detected, then the mask cannot be extracted.  That may be what happens when you set 0/0.5/1.  The default 100 should work fine, but adjust if necessary based on your scanning parameters.

If the above suggestion does not help, please send the error messages ("View" menu -> "Error Log"), and find out whether you can share a *anonymized* version of a typical dataset for us to investigate.

Best,
Isaiah

On Mon, Jul 25, 2016 at 11:45 AM, Luca Fumagalli <[hidden email]> wrote:
Good morning,

I am having some problems regarding the creation of a brain mask before estimating the tensor.

I am using 3DSlicer 4.5.0-1. I followed the instructions in DiffusionMRIanalysisTutorial, but when I had to create the brain mask, I noticed that instead of "Baseline B-value threshold parameter", there was "Otsu omega threshold parameter". I tried to run the "apply" command after setting the otsu omega parameter to 0, 0.1, 0.5 (default) and 1. Every time, the result is "Status: completed with errors" and the mask doesn't appear.

Please let me know if you could help me with this impasse.

Regards,

Luca

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




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unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error

Audette, Michel A.

Dear Slicer users, 


I have been trying unsuccessfully to build Bender on MS Visual C++ 2012, and it is failing in the Slicer portion at the point of KTKVtkGlue. 


2>    CMake Error at C:/Bender/BenderBuild/Slicer-build/ITKv4/CMake/ITKModuleAPI.cmake:50 (message):
2>      No such module: "ITKVtkGlue"

I am mostly interested in this build to see how SOFA interacts with a calling program: do I absolutely need ITKVtkGlue in that case? 


If I can dispense with it, what is the appropriate instruction for CMAKE? 


I tried the following in the Slicer file in Superbuild,       -DModule_ITKVtkGlue:BOOL=OFF , but that did not seem to work. 


Thanks for your kind support. Please advise. 


Michel


Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.

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Re: unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error

Andras Lasso-2

Have you tried to build Bender with the recommended build options (probably VS2008)?

 

Have you changed any build options (e.g., ITK version, …)?

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Audette, Michel A.
Sent: August 1, 2016 14:42
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error

 

Dear Slicer users, 

 

I have been trying unsuccessfully to build Bender on MS Visual C++ 2012, and it is failing in the Slicer portion at the point of KTKVtkGlue. 

 

2>    CMake Error at C:/Bender/BenderBuild/Slicer-build/ITKv4/CMake/ITKModuleAPI.cmake:50 (message):

2>      No such module: "ITKVtkGlue"

 

I am mostly interested in this build to see how SOFA interacts with a calling program: do I absolutely need ITKVtkGlue in that case? 

 

If I can dispense with it, what is the appropriate instruction for CMAKE? 

 

I tried the following in the Slicer file in Superbuild,       -DModule_ITKVtkGlue:BOOL=OFF , but that did not seem to work. 

 

Thanks for your kind support. Please advise. 

 

Michel

 

Michel Audette, Ph.D.

Assistant Professor,

Department of Modeling, Simulation and Visualization Engineering,

Old Dominion University,

Norfolk, VA.


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Re: unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error

Audette, Michel A.
In reply to this post by Audette, Michel A.

Hi Andras, 


no I have not. The only thing that I did was to add the following to Slicer CMake file in Superbuild  to get rid of pre-existing errors. 

-D${proj}_USE_NUMPY:BOOL=OFF
-D${proj}_USE_SimpleITK:BOOL=OFF
      -DModule_ITKVtkGlue:BOOL=OFF

If you say that it builds with VS2008, I will give it a try. Thanks for your support. 


Best wishes,


Michel


Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
 

From: Andras Lasso <[hidden email]>
Sent: Monday, August 1, 2016 3:39:21 PM
To: Audette, Michel A.; SPL Slicer Users
Subject: RE: unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error
 

Have you tried to build Bender with the recommended build options (probably VS2008)?

 

Have you changed any build options (e.g., ITK version, …)?

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Audette, Michel A.
Sent: August 1, 2016 14:42
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error

 

Dear Slicer users, 

 

I have been trying unsuccessfully to build Bender on MS Visual C++ 2012, and it is failing in the Slicer portion at the point of KTKVtkGlue. 

 

2>    CMake Error at C:/Bender/BenderBuild/Slicer-build/ITKv4/CMake/ITKModuleAPI.cmake:50 (message):

2>      No such module: "ITKVtkGlue"

 

I am mostly interested in this build to see how SOFA interacts with a calling program: do I absolutely need ITKVtkGlue in that case? 

 

If I can dispense with it, what is the appropriate instruction for CMAKE? 

 

I tried the following in the Slicer file in Superbuild,       -DModule_ITKVtkGlue:BOOL=OFF , but that did not seem to work. 

 

Thanks for your kind support. Please advise. 

 

Michel

 

Michel Audette, Ph.D.

Assistant Professor,

Department of Modeling, Simulation and Visualization Engineering,

Old Dominion University,

Norfolk, VA.


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Re: unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error

Andrey Fedorov-2
Did you try contacting the Bender support? 

It is an application that is based on some version of Slicer, but I don’t know how it is related to the current Slicer code base.


On Aug 1, 2016, at 3:51 PM, Audette, Michel A. <[hidden email]> wrote:

Hi Andras, 

no I have not. The only thing that I did was to add the following to Slicer CMake file in Superbuild  to get rid of pre-existing errors. 

-D${proj}_USE_NUMPY:BOOL=OFF
-D${proj}_USE_SimpleITK:BOOL=OFF
      -DModule_ITKVtkGlue:BOOL=OFF

If you say that it builds with VS2008, I will give it a try. Thanks for your support. 

Best wishes,

Michel

Michel Audette, Ph.D. 
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
 

From: Andras Lasso <[hidden email]>
Sent: Monday, August 1, 2016 3:39:21 PM
To: Audette, Michel A.; SPL Slicer Users
Subject: RE: unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error
 
Have you tried to build Bender with the recommended build options (probably VS2008)?
 
Have you changed any build options (e.g., ITK version, …)?
 
Andras
From: slicer-users [[hidden email]] On Behalf Of Audette, Michel A.
Sent: August 1, 2016 14:42
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error
 
Dear Slicer users, 
 
I have been trying unsuccessfully to build Bender on MS Visual C++ 2012, and it is failing in the Slicer portion at the point of KTKVtkGlue. 
 
2>    CMake Error at C:/Bender/BenderBuild/Slicer-build/ITKv4/CMake/ITKModuleAPI.cmake:50 (message):
2>      No such module: "ITKVtkGlue"
 
I am mostly interested in this build to see how SOFA interacts with a calling program: do I absolutely need ITKVtkGlue in that case? 
 
If I can dispense with it, what is the appropriate instruction for CMAKE? 
 
I tried the following in the Slicer file in Superbuild,       -DModule_ITKVtkGlue:BOOL=OFF , but that did not seem to work. 
 
Thanks for your kind support. Please advise. 
 
Michel
 
Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
_______________________________________________
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


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Re: unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error

Andras Lasso-2
In reply to this post by Audette, Michel A.

According to http://public.kitware.com/Wiki/Bender/Installation#Installing_from_source, prerequisites of compiler and tools are described here:

https://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Developers/Build_Instructions/Prerequisites

 

Julien Finet (http://www.kitware.com/company/team/finet.html) might also be able to give advice, he was the main developer of Bender.

 

Andras

 

From: Audette, Michel A. [mailto:[hidden email]]
Sent: August 1, 2016 15:51
To: Andras Lasso <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error

 

Hi Andras, 

 

no I have not. The only thing that I did was to add the following to Slicer CMake file in Superbuild  to get rid of pre-existing errors. 

-D${proj}_USE_NUMPY:BOOL=OFF

-D${proj}_USE_SimpleITK:BOOL=OFF

      -DModule_ITKVtkGlue:BOOL=OFF

 

If you say that it builds with VS2008, I will give it a try. Thanks for your support. 

 

Best wishes,

 

Michel

 

Michel Audette, Ph.D.

Assistant Professor,

Department of Modeling, Simulation and Visualization Engineering,

Old Dominion University,

Norfolk, VA.

 


From: Andras Lasso <[hidden email]>
Sent: Monday, August 1, 2016 3:39:21 PM
To: Audette, Michel A.; SPL Slicer Users
Subject: RE: unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error

 

Have you tried to build Bender with the recommended build options (probably VS2008)?

 

Have you changed any build options (e.g., ITK version, …)?

 

Andras

 

From: slicer-users [[hidden email]] On Behalf Of Audette, Michel A.
Sent: August 1, 2016 14:42
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error

 

Dear Slicer users, 

 

I have been trying unsuccessfully to build Bender on MS Visual C++ 2012, and it is failing in the Slicer portion at the point of KTKVtkGlue. 

 

2>    CMake Error at C:/Bender/BenderBuild/Slicer-build/ITKv4/CMake/ITKModuleAPI.cmake:50 (message):

2>      No such module: "ITKVtkGlue"

 

I am mostly interested in this build to see how SOFA interacts with a calling program: do I absolutely need ITKVtkGlue in that case? 

 

If I can dispense with it, what is the appropriate instruction for CMAKE? 

 

I tried the following in the Slicer file in Superbuild,       -DModule_ITKVtkGlue:BOOL=OFF , but that did not seem to work. 

 

Thanks for your kind support. Please advise. 

 

Michel

 

Michel Audette, Ph.D.

Assistant Professor,

Department of Modeling, Simulation and Visualization Engineering,

Old Dominion University,

Norfolk, VA.


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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error

Audette, Michel A.
In reply to this post by Audette, Michel A.

Hi Andrey, 


yes I have. I've tried to locate who it is who is providing support right now. I think that some of the senior guys are on holidays so my timing is not very good. I've been interacting with Julien Finet a little, but I'm not sure to what extent he is providing support officially. I have not heard from him today. It's tricky with the time difference, with him in France.


At this point, it looks like VS 2008 is the best way forward. 


Michel


Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
 

From: Andrey Fedorov <[hidden email]>
Sent: Monday, August 1, 2016 3:54:43 PM
To: Audette, Michel A.
Cc: Andras Lasso; SPL Slicer Users
Subject: Re: [slicer-users] unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error
 
Did you try contacting the Bender support? 

It is an application that is based on some version of Slicer, but I don’t know how it is related to the current Slicer code base.


On Aug 1, 2016, at 3:51 PM, Audette, Michel A. <[hidden email]> wrote:

Hi Andras, 

no I have not. The only thing that I did was to add the following to Slicer CMake file in Superbuild  to get rid of pre-existing errors. 

-D${proj}_USE_NUMPY:BOOL=OFF
-D${proj}_USE_SimpleITK:BOOL=OFF
      -DModule_ITKVtkGlue:BOOL=OFF

If you say that it builds with VS2008, I will give it a try. Thanks for your support. 

Best wishes,

Michel

Michel Audette, Ph.D. 
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
 

From: Andras Lasso <[hidden email]>
Sent: Monday, August 1, 2016 3:39:21 PM
To: Audette, Michel A.; SPL Slicer Users
Subject: RE: unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error
 
Have you tried to build Bender with the recommended build options (probably VS2008)?
 
Have you changed any build options (e.g., ITK version, …)?
 
Andras
From: slicer-users [[hidden email]] On Behalf Of Audette, Michel A.
Sent: August 1, 2016 14:42
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error
 
Dear Slicer users, 
 
I have been trying unsuccessfully to build Bender on MS Visual C++ 2012, and it is failing in the Slicer portion at the point of KTKVtkGlue. 
 
2>    CMake Error at C:/Bender/BenderBuild/Slicer-build/ITKv4/CMake/ITKModuleAPI.cmake:50 (message):
2>      No such module: "ITKVtkGlue"
 
I am mostly interested in this build to see how SOFA interacts with a calling program: do I absolutely need ITKVtkGlue in that case? 
 
If I can dispense with it, what is the appropriate instruction for CMAKE? 
 
I tried the following in the Slicer file in Superbuild,       -DModule_ITKVtkGlue:BOOL=OFF , but that did not seem to work. 
 
Thanks for your kind support. Please advise. 
 
Michel
 
Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


_______________________________________________
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error

Steve Pieper-2
Hi Michel -

Yes, I believe vs2008 was the only viable compiler at the time Bender was developed.  I don't know if it's been ported to later versions of Slicer/VTK/etc.

Best,
Steve

On Mon, Aug 1, 2016 at 3:59 PM, Audette, Michel A. <[hidden email]> wrote:

Hi Andrey, 


yes I have. I've tried to locate who it is who is providing support right now. I think that some of the senior guys are on holidays so my timing is not very good. I've been interacting with Julien Finet a little, but I'm not sure to what extent he is providing support officially. I have not heard from him today. It's tricky with the time difference, with him in France.


At this point, it looks like VS 2008 is the best way forward. 


Michel


Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
 

From: Andrey Fedorov <[hidden email]>
Sent: Monday, August 1, 2016 3:54:43 PM
To: Audette, Michel A.
Cc: Andras Lasso; SPL Slicer Users
Subject: Re: [slicer-users] unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error
 
Did you try contacting the Bender support? 

It is an application that is based on some version of Slicer, but I don’t know how it is related to the current Slicer code base.


On Aug 1, 2016, at 3:51 PM, Audette, Michel A. <[hidden email]> wrote:

Hi Andras, 

no I have not. The only thing that I did was to add the following to Slicer CMake file in Superbuild  to get rid of pre-existing errors. 

-D${proj}_USE_NUMPY:BOOL=OFF
-D${proj}_USE_SimpleITK:BOOL=OFF
      -DModule_ITKVtkGlue:BOOL=OFF

If you say that it builds with VS2008, I will give it a try. Thanks for your support. 

Best wishes,

Michel

Michel Audette, Ph.D. 
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
 

From: Andras Lasso <[hidden email]>
Sent: Monday, August 1, 2016 3:39:21 PM
To: Audette, Michel A.; SPL Slicer Users
Subject: RE: unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error
 
Have you tried to build Bender with the recommended build options (probably VS2008)?
 
Have you changed any build options (e.g., ITK version, …)?
 
Andras
From: slicer-users [[hidden email]] On Behalf Of Audette, Michel A.
Sent: August 1, 2016 14:42
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error
 
Dear Slicer users, 
 
I have been trying unsuccessfully to build Bender on MS Visual C++ 2012, and it is failing in the Slicer portion at the point of KTKVtkGlue. 
 
2>    CMake Error at C:/Bender/BenderBuild/Slicer-build/ITKv4/CMake/ITKModuleAPI.cmake:50 (message):
2>      No such module: "ITKVtkGlue"
 
I am mostly interested in this build to see how SOFA interacts with a calling program: do I absolutely need ITKVtkGlue in that case? 
 
If I can dispense with it, what is the appropriate instruction for CMAKE? 
 
I tried the following in the Slicer file in Superbuild,       -DModule_ITKVtkGlue:BOOL=OFF , but that did not seem to work. 
 
Thanks for your kind support. Please advise. 
 
Michel
 
Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
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Re: unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error

Audette, Michel A.
In reply to this post by Audette, Michel A.

Hi gents and Slicer users, 


Steve, thanks for your kind reply. 


I'm making progress after installing MSVC 2008, supplemented by a MS Service Pack. 


Currently, I am down to 4 errors, which are difficult for me to parse. All of them are of the type:  

Error 809 error PRJ0019: A tool returned an error code from "Performing configure step for 'Slicer'"


Is this an easy one to stamp out? 


Michel

Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
 

From: Steve Pieper <[hidden email]>
Sent: Monday, August 1, 2016 5:50:52 PM
To: Audette, Michel A.
Cc: Andrey Fedorov; SPL Slicer Users
Subject: Re: [slicer-users] unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error
 
Hi Michel -

Yes, I believe vs2008 was the only viable compiler at the time Bender was developed.  I don't know if it's been ported to later versions of Slicer/VTK/etc.

Best,
Steve

On Mon, Aug 1, 2016 at 3:59 PM, Audette, Michel A. <[hidden email]> wrote:

Hi Andrey, 


yes I have. I've tried to locate who it is who is providing support right now. I think that some of the senior guys are on holidays so my timing is not very good. I've been interacting with Julien Finet a little, but I'm not sure to what extent he is providing support officially. I have not heard from him today. It's tricky with the time difference, with him in France.


At this point, it looks like VS 2008 is the best way forward. 


Michel


Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
 

From: Andrey Fedorov <[hidden email]>
Sent: Monday, August 1, 2016 3:54:43 PM
To: Audette, Michel A.
Cc: Andras Lasso; SPL Slicer Users
Subject: Re: [slicer-users] unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error
 
Did you try contacting the Bender support? 

It is an application that is based on some version of Slicer, but I don’t know how it is related to the current Slicer code base.


On Aug 1, 2016, at 3:51 PM, Audette, Michel A. <[hidden email]> wrote:

Hi Andras, 

no I have not. The only thing that I did was to add the following to Slicer CMake file in Superbuild  to get rid of pre-existing errors. 

-D${proj}_USE_NUMPY:BOOL=OFF
-D${proj}_USE_SimpleITK:BOOL=OFF
      -DModule_ITKVtkGlue:BOOL=OFF

If you say that it builds with VS2008, I will give it a try. Thanks for your support. 

Best wishes,

Michel

Michel Audette, Ph.D. 
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
 

From: Andras Lasso <[hidden email]>
Sent: Monday, August 1, 2016 3:39:21 PM
To: Audette, Michel A.; SPL Slicer Users
Subject: RE: unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error
 
Have you tried to build Bender with the recommended build options (probably VS2008)?
 
Have you changed any build options (e.g., ITK version, …)?
 
Andras
From: slicer-users [[hidden email]] On Behalf Of Audette, Michel A.
Sent: August 1, 2016 14:42
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error
 
Dear Slicer users, 
 
I have been trying unsuccessfully to build Bender on MS Visual C++ 2012, and it is failing in the Slicer portion at the point of KTKVtkGlue. 
 
2>    CMake Error at C:/Bender/BenderBuild/Slicer-build/ITKv4/CMake/ITKModuleAPI.cmake:50 (message):
2>      No such module: "ITKVtkGlue"
 
I am mostly interested in this build to see how SOFA interacts with a calling program: do I absolutely need ITKVtkGlue in that case? 
 
If I can dispense with it, what is the appropriate instruction for CMAKE? 
 
I tried the following in the Slicer file in Superbuild,       -DModule_ITKVtkGlue:BOOL=OFF , but that did not seem to work. 
 
Thanks for your kind support. Please advise. 
 
Michel
 
Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error

Steve Pieper-2
In reply to this post by Audette, Michel A.
Hi Michel - 

I'm afraid that one looks pretty mysterious.  Something in cmake but it could take some serious digging to figure it out.  I never worked on Bender but I'm guessing it might be easier to port to the latest Slicer than to try maintaining the old build environment.

Best of luck!
-Steve

On Fri, Aug 5, 2016 at 11:09 AM, Audette, Michel A. <[hidden email]> wrote:

Hi gents and Slicer users, 


Steve, thanks for your kind reply. 


I'm making progress after installing MSVC 2008, supplemented by a MS Service Pack. 


Currently, I am down to 4 errors, which are difficult for me to parse. All of them are of the type:  

Error 809 error PRJ0019: A tool returned an error code from "Performing configure step for 'Slicer'"


Is this an easy one to stamp out? 


Michel

Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
 

From: Steve Pieper <[hidden email]>
Sent: Monday, August 1, 2016 5:50:52 PM
To: Audette, Michel A.
Cc: Andrey Fedorov; SPL Slicer Users

Subject: Re: [slicer-users] unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error
 
Hi Michel -

Yes, I believe vs2008 was the only viable compiler at the time Bender was developed.  I don't know if it's been ported to later versions of Slicer/VTK/etc.

Best,
Steve

On Mon, Aug 1, 2016 at 3:59 PM, Audette, Michel A. <[hidden email]> wrote:

Hi Andrey, 


yes I have. I've tried to locate who it is who is providing support right now. I think that some of the senior guys are on holidays so my timing is not very good. I've been interacting with Julien Finet a little, but I'm not sure to what extent he is providing support officially. I have not heard from him today. It's tricky with the time difference, with him in France.


At this point, it looks like VS 2008 is the best way forward. 


Michel


Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
 

From: Andrey Fedorov <[hidden email]>
Sent: Monday, August 1, 2016 3:54:43 PM
To: Audette, Michel A.
Cc: Andras Lasso; SPL Slicer Users
Subject: Re: [slicer-users] unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error
 
Did you try contacting the Bender support? 

It is an application that is based on some version of Slicer, but I don’t know how it is related to the current Slicer code base.


On Aug 1, 2016, at 3:51 PM, Audette, Michel A. <[hidden email]> wrote:

Hi Andras, 

no I have not. The only thing that I did was to add the following to Slicer CMake file in Superbuild  to get rid of pre-existing errors. 

-D${proj}_USE_NUMPY:BOOL=OFF
-D${proj}_USE_SimpleITK:BOOL=OFF
      -DModule_ITKVtkGlue:BOOL=OFF

If you say that it builds with VS2008, I will give it a try. Thanks for your support. 

Best wishes,

Michel

Michel Audette, Ph.D. 
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
 

From: Andras Lasso <[hidden email]>
Sent: Monday, August 1, 2016 3:39:21 PM
To: Audette, Michel A.; SPL Slicer Users
Subject: RE: unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error
 
Have you tried to build Bender with the recommended build options (probably VS2008)?
 
Have you changed any build options (e.g., ITK version, …)?
 
Andras
From: slicer-users [[hidden email]] On Behalf Of Audette, Michel A.
Sent: August 1, 2016 14:42
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error
 
Dear Slicer users, 
 
I have been trying unsuccessfully to build Bender on MS Visual C++ 2012, and it is failing in the Slicer portion at the point of KTKVtkGlue. 
 
2>    CMake Error at C:/Bender/BenderBuild/Slicer-build/ITKv4/CMake/ITKModuleAPI.cmake:50 (message):
2>      No such module: "ITKVtkGlue"
 
I am mostly interested in this build to see how SOFA interacts with a calling program: do I absolutely need ITKVtkGlue in that case? 
 
If I can dispense with it, what is the appropriate instruction for CMAKE? 
 
I tried the following in the Slicer file in Superbuild,       -DModule_ITKVtkGlue:BOOL=OFF , but that did not seem to work. 
 
Thanks for your kind support. Please advise. 
 
Michel
 
Michel Audette, Ph.D.
Assistant Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


_______________________________________________
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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ



_______________________________________________
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[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: unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error

Andras Lasso-2

The exact failure is probably described in log files within the Slicer project directory (in Slicer-build, most likely in Slicer-build\Testing).

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Steve Pieper
Sent: August 5, 2016 12:06
To: Audette, Michel A. <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error

 

Hi Michel - 

 

I'm afraid that one looks pretty mysterious.  Something in cmake but it could take some serious digging to figure it out.  I never worked on Bender but I'm guessing it might be easier to port to the latest Slicer than to try maintaining the old build environment.

 

Best of luck!

-Steve

 

On Fri, Aug 5, 2016 at 11:09 AM, Audette, Michel A. <[hidden email]> wrote:

Hi gents and Slicer users, 

 

Steve, thanks for your kind reply. 

 

I'm making progress after installing MSVC 2008, supplemented by a MS Service Pack. 

 

Currently, I am down to 4 errors, which are difficult for me to parse. All of them are of the type:  

Error 809 error PRJ0019: A tool returned an error code from "Performing configure step for 'Slicer'"

 

Is this an easy one to stamp out? 

 

Michel

Michel Audette, Ph.D.

Assistant Professor,

Department of Modeling, Simulation and Visualization Engineering,

Old Dominion University,

Norfolk, VA.

 


From: Steve Pieper <[hidden email]>
Sent: Monday, August 1, 2016 5:50:52 PM
To: Audette, Michel A.
Cc: Andrey Fedorov; SPL Slicer Users


Subject: Re: [slicer-users] unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error

 

Hi Michel -

 

Yes, I believe vs2008 was the only viable compiler at the time Bender was developed.  I don't know if it's been ported to later versions of Slicer/VTK/etc.

 

Best,

Steve

 

On Mon, Aug 1, 2016 at 3:59 PM, Audette, Michel A. <[hidden email]> wrote:

Hi Andrey, 

 

yes I have. I've tried to locate who it is who is providing support right now. I think that some of the senior guys are on holidays so my timing is not very good. I've been interacting with Julien Finet a little, but I'm not sure to what extent he is providing support officially. I have not heard from him today. It's tricky with the time difference, with him in France.

 

At this point, it looks like VS 2008 is the best way forward. 

 

Michel

 

Michel Audette, Ph.D.

Assistant Professor,

Department of Modeling, Simulation and Visualization Engineering,

Old Dominion University,

Norfolk, VA.

 


From: Andrey Fedorov <[hidden email]>
Sent: Monday, August 1, 2016 3:54:43 PM
To: Audette, Michel A.
Cc: Andras Lasso; SPL Slicer Users
Subject: Re: [slicer-users] unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error

 

Did you try contacting the Bender support? 

 

It is an application that is based on some version of Slicer, but I don’t know how it is related to the current Slicer code base.

 

 

On Aug 1, 2016, at 3:51 PM, Audette, Michel A. <[hidden email]> wrote:

 

Hi Andras, 

 

no I have not. The only thing that I did was to add the following to Slicer CMake file in Superbuild  to get rid of pre-existing errors. 

-D${proj}_USE_NUMPY:BOOL=OFF

-D${proj}_USE_SimpleITK:BOOL=OFF

      -DModule_ITKVtkGlue:BOOL=OFF

 

If you say that it builds with VS2008, I will give it a try. Thanks for your support. 

 

Best wishes,

 

Michel

 

Michel Audette, Ph.D. 

Assistant Professor,

Department of Modeling, Simulation and Visualization Engineering,

Old Dominion University,

Norfolk, VA.

 


From: Andras Lasso <[hidden email]>
Sent: Monday, August 1, 2016 3:39:21 PM
To: Audette, Michel A.; SPL Slicer Users
Subject: RE: unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error

 

Have you tried to build Bender with the recommended build options (probably VS2008)?

 

Have you changed any build options (e.g., ITK version, …)?

 

Andras

 

From: slicer-users [[hidden email]On Behalf Of Audette, Michel A.
Sent: August 1, 2016 14:42
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] unable to get Slicer portion of Bender to build on MSVC 2012 , due to ITKVtkGlue error

 

Dear Slicer users, 

 

I have been trying unsuccessfully to build Bender on MS Visual C++ 2012, and it is failing in the Slicer portion at the point of KTKVtkGlue. 

 

2>    CMake Error at C:/Bender/BenderBuild/Slicer-build/ITKv4/CMake/ITKModuleAPI.cmake:50 (message):

2>      No such module: "ITKVtkGlue"

 

I am mostly interested in this build to see how SOFA interacts with a calling program: do I absolutely need ITKVtkGlue in that case? 

 

If I can dispense with it, what is the appropriate instruction for CMAKE? 

 

I tried the following in the Slicer file in Superbuild,       -DModule_ITKVtkGlue:BOOL=OFF , but that did not seem to work. 

 

Thanks for your kind support. Please advise. 

 

Michel

 

Michel Audette, Ph.D.

Assistant Professor,

Department of Modeling, Simulation and Visualization Engineering,

Old Dominion University,

Norfolk, VA.

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to 
[hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ

 


_______________________________________________
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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ

 

 


_______________________________________________
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[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