EMSegmentCommandLine errors

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EMSegmentCommandLine errors

madanrao
Hello all,

I am trying to run the Segmentation on EMSegmentCommandLine.exe from cmd or cygwin on windows vista using the tutorial data.

I get the following error:

ERROR: In ..\..\..\Slicer3\Libs\MRML\vtkMRMLColorTableStorageNode.cxx, line 255
vtkMRMLColorTableStorageNode (04C3CE90): ERROR opening colour file /home/rao/share/FreeSurfer/FreeSurferColorLUT.txt

I have Slicer3-build using Cygwin. I am able to run the --help command from the EMSegmentCommndLine.exe after adding about 48 *.dll files
to my system32 library.

Can anyone help please?

AM Mohan Rao



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Re: EMSegmentCommandLine errors

madanrao
Hello all,

I also tried running the exe after creating the path in the error and keeping the txt file with no result.

AM Mohan Rao

On Tue, Mar 16, 2010 at 1:03 PM, Madan Rao <[hidden email]> wrote:
Hello all,

I am trying to run the Segmentation on EMSegmentCommandLine.exe from cmd or cygwin on windows vista using the tutorial data.

I get the following error:

ERROR: In ..\..\..\Slicer3\Libs\MRML\vtkMRMLColorTableStorageNode.cxx, line 255
vtkMRMLColorTableStorageNode (04C3CE90): ERROR opening colour file /home/rao/share/FreeSurfer/FreeSurferColorLUT.txt

I have Slicer3-build using Cygwin. I am able to run the --help command from the EMSegmentCommndLine.exe after adding about 48 *.dll files
to my system32 library.

Can anyone help please?

AM Mohan Rao




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Re: EMSegmentCommandLine errors

pieper
Administrator
Hi Mohan -

I'm not sure about the color file issue (perhaps Nicole knows).

But for the dll issue you should be able to run a command like:

  <path to>/Slicer3.exe --launch EMSegmentCommandLine.exe

this will set up the paths for you so you don't need to copy anything to
the system directories.

Best,
Steve

On M/16/10 3:41 AM, Madan Rao wrote:

> Hello all,
>
> I also tried running the exe after creating the path in the error and
> keeping the txt file with no result.
>
> AM Mohan Rao
>
> On Tue, Mar 16, 2010 at 1:03 PM, Madan Rao <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hello all,
>
>     I am trying to run the Segmentation on EMSegmentCommandLine.exe from
>     cmd or cygwin on windows vista using the tutorial data.
>
>     I get the following error:
>
>     ERROR: In
>     ..\..\..\Slicer3\Libs\MRML\vtkMRMLColorTableStorageNode.cxx, line 255
>     vtkMRMLColorTableStorageNode (04C3CE90): ERROR opening colour file
>     /home/rao/share/FreeSurfer/FreeSurferColorLUT.txt
>
>     I have Slicer3-build using Cygwin. I am able to run the --help
>     command from the EMSegmentCommndLine.exe after adding about 48 *.dll
>     files
>     to my system32 library.
>
>     Can anyone help please?
>
>     AM Mohan Rao
>
>
>
>
>
> _______________________________________________
> 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: EMSegmentCommandLine errors

madanrao
Hello Steve,

Thanks. It seems to be working now by following your suggestion.

However, I cant get the --help running from cmd by:

Slicer3 --launch EMSegmentCommandLine --help

Can you explain it?

AM Mohan Rao


On Tue, Mar 16, 2010 at 3:31 PM, Steve Pieper <[hidden email]> wrote:
Hi Mohan -

I'm not sure about the color file issue (perhaps Nicole knows).

But for the dll issue you should be able to run a command like:

 <path to>/Slicer3.exe --launch EMSegmentCommandLine.exe

this will set up the paths for you so you don't need to copy anything to the system directories.

Best,
Steve


On M/16/10 3:41 AM, Madan Rao wrote:
Hello all,

I also tried running the exe after creating the path in the error and
keeping the txt file with no result.

AM Mohan Rao

On Tue, Mar 16, 2010 at 1:03 PM, Madan Rao <[hidden email]
<mailto:[hidden email]>> wrote:

   Hello all,

   I am trying to run the Segmentation on EMSegmentCommandLine.exe from
   cmd or cygwin on windows vista using the tutorial data.

   I get the following error:

   ERROR: In
   ..\..\..\Slicer3\Libs\MRML\vtkMRMLColorTableStorageNode.cxx, line 255
   vtkMRMLColorTableStorageNode (04C3CE90): ERROR opening colour file
   /home/rao/share/FreeSurfer/FreeSurferColorLUT.txt

   I have Slicer3-build using Cygwin. I am able to run the --help
   command from the EMSegmentCommndLine.exe after adding about 48 *.dll
   files
   to my system32 library.

   Can anyone help please?

   AM Mohan Rao





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Re: EMSegmentCommandLine errors

madanrao
Hello,

What is the input for EMSegmentCommandLine atlas data?

If I give:

Slicer3 --launch EMSegmentCommandLine --mrmlSceneFileName <path to EMSegmentTutorialTemplate.mhd>
--resultMRMLSceneFileName <path to segmentation.mhd> --targetVolumeFileNames <path to target_t1_normed.mhd,target_t2_normed.mhd> --atlasVolumeFileNames <path to atlas_background_reg.mhd,atlas_csf_reg.mhd,atlas_greymatter_reg,atlas_whitematter_reg.mhd>

I get the error:

parameters must already contain an atlas node if you wish to specify atlas volumes..

I cannot understand the --parametersMRMLNodeName in this context. If I don't give atlas paths I get the error:

No default atlas node is available.

Please help.

AM Mohan Rao

On Tue, Mar 16, 2010 at 6:52 PM, Madan Rao <[hidden email]> wrote:
Hello Steve,

Thanks. It seems to be working now by following your suggestion.

However, I cant get the --help running from cmd by:

Slicer3 --launch EMSegmentCommandLine --help

Can you explain it?

AM Mohan Rao



On Tue, Mar 16, 2010 at 3:31 PM, Steve Pieper <[hidden email]> wrote:
Hi Mohan -

I'm not sure about the color file issue (perhaps Nicole knows).

But for the dll issue you should be able to run a command like:

 <path to>/Slicer3.exe --launch EMSegmentCommandLine.exe

this will set up the paths for you so you don't need to copy anything to the system directories.

Best,
Steve


On M/16/10 3:41 AM, Madan Rao wrote:
Hello all,

I also tried running the exe after creating the path in the error and
keeping the txt file with no result.

AM Mohan Rao

On Tue, Mar 16, 2010 at 1:03 PM, Madan Rao <[hidden email]
<mailto:[hidden email]>> wrote:

   Hello all,

   I am trying to run the Segmentation on EMSegmentCommandLine.exe from
   cmd or cygwin on windows vista using the tutorial data.

   I get the following error:

   ERROR: In
   ..\..\..\Slicer3\Libs\MRML\vtkMRMLColorTableStorageNode.cxx, line 255
   vtkMRMLColorTableStorageNode (04C3CE90): ERROR opening colour file
   /home/rao/share/FreeSurfer/FreeSurferColorLUT.txt

   I have Slicer3-build using Cygwin. I am able to run the --help
   command from the EMSegmentCommndLine.exe after adding about 48 *.dll
   files
   to my system32 library.

   Can anyone help please?

   AM Mohan Rao





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slicer-users mailing list
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Re: EMSegmentCommandLine errors

Aucoin, Nicole
Hello,

I'd strongly suggest running it once from the Slicer GUI, then looking
at the Error Log to see the full command line that it passes.
The mrml scene files end in .mrml and contain node tags that will allow
slicer to reload the output scene (including volumes).

Nicole

Madan Rao wrote:

> Hello,
>
> What is the input for EMSegmentCommandLine atlas data?
>
> If I give:
>
> Slicer3 --launch EMSegmentCommandLine --mrmlSceneFileName <path to
> EMSegmentTutorialTemplate.mhd>
> --resultMRMLSceneFileName <path to segmentation.mhd>
> --targetVolumeFileNames <path to
> target_t1_normed.mhd,target_t2_normed.mhd> --atlasVolumeFileNames
> <path to
> atlas_background_reg.mhd,atlas_csf_reg.mhd,atlas_greymatter_reg,atlas_whitematter_reg.mhd>
>
> I get the error:
>
> parameters must already contain an atlas node if you wish to specify
> atlas volumes..
>
> I cannot understand the --parametersMRMLNodeName in this context. If I
> don't give atlas paths I get the error:
>
> No default atlas node is available.
>
> Please help.
>
> AM Mohan Rao
>
> On Tue, Mar 16, 2010 at 6:52 PM, Madan Rao <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hello Steve,
>
>     Thanks. It seems to be working now by following your suggestion.
>
>     However, I cant get the --help running from cmd by:
>
>     Slicer3 --launch EMSegmentCommandLine --help
>
>     Can you explain it?
>
>     AM Mohan Rao
>
>
>
>     On Tue, Mar 16, 2010 at 3:31 PM, Steve Pieper
>     <[hidden email] <mailto:[hidden email]>> wrote:
>
>         Hi Mohan -
>
>         I'm not sure about the color file issue (perhaps Nicole knows).
>
>         But for the dll issue you should be able to run a command like:
>
>          <path to>/Slicer3.exe --launch EMSegmentCommandLine.exe
>
>         this will set up the paths for you so you don't need to copy
>         anything to the system directories.
>
>         Best,
>         Steve
>
>
>         On M/16/10 3:41 AM, Madan Rao wrote:
>
>             Hello all,
>
>             I also tried running the exe after creating the path in
>             the error and
>             keeping the txt file with no result.
>
>             AM Mohan Rao
>
>             On Tue, Mar 16, 2010 at 1:03 PM, Madan Rao
>             <[hidden email] <mailto:[hidden email]>
>             <mailto:[hidden email] <mailto:[hidden email]>>> wrote:
>
>                Hello all,
>
>                I am trying to run the Segmentation on
>             EMSegmentCommandLine.exe from
>                cmd or cygwin on windows vista using the tutorial data.
>
>                I get the following error:
>
>                ERROR: In
>              
>              ..\..\..\Slicer3\Libs\MRML\vtkMRMLColorTableStorageNode.cxx,
>             line 255
>                vtkMRMLColorTableStorageNode (04C3CE90): ERROR opening
>             colour file
>                /home/rao/share/FreeSurfer/FreeSurferColorLUT.txt
>
>                I have Slicer3-build using Cygwin. I am able to run the
>             --help
>                command from the EMSegmentCommndLine.exe after adding
>             about 48 *.dll
>                files
>                to my system32 library.
>
>                Can anyone help please?
>
>                AM Mohan Rao
>
>
>
>
>
>             _______________________________________________
>             slicer-users mailing list
>             [hidden email]
>             <mailto:[hidden email]>
>             http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>             To unsubscribe: send email to
>             [hidden email]
>             <mailto:[hidden email]>
>             with unsubscribe as the subject
>
>
>
> ------------------------------------------------------------------------
>
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> slicer-users mailing list
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Re: EMSegmentCommandLine errors

madanrao
Hello Nicole,

Thanks.

Automatic segmentation by Sonia Pujole works well and I do not expect any errors from the tutorial data.

What I am trying for is few workable example code for its command line version..

I assume:  --targetVolumeFileNames target_t1.mhd,target_t2.mhd.
--atlasVolumeFileNames atlas_background.mhd,atlas_csf.mhd,atlas_greymatter.mhd,atlas_whitematter.mhd.
--mrmlSceneFileName EMSegmentParameters..

I think to run EMSegmentCommandLine one needs to start off with Slicer3 GUI and follow automatic segmentation methods as
described upto the stage of running the final EMSegmentation process.

Or if I am wrong please let me know.

I have already logged in some 600 hrs doing automatic segmentation and I really want to take off with the command line.
I would definitely try your suggestion but I am not sure whether it helps me now.

regards,

AM Mohan Rao



On Tue, Mar 16, 2010 at 8:28 PM, Nicole Aucoin <[hidden email]> wrote:
Hello,

I'd strongly suggest running it once from the Slicer GUI, then looking at the Error Log to see the full command line that it passes.
The mrml scene files end in .mrml and contain node tags that will allow slicer to reload the output scene (including volumes).

Nicole

Madan Rao wrote:
Hello,

What is the input for EMSegmentCommandLine atlas data?

If I give:

Slicer3 --launch EMSegmentCommandLine --mrmlSceneFileName <path to EMSegmentTutorialTemplate.mhd>
--resultMRMLSceneFileName <path to segmentation.mhd> --targetVolumeFileNames <path to target_t1_normed.mhd,target_t2_normed.mhd> --atlasVolumeFileNames <path to atlas_background_reg.mhd,atlas_csf_reg.mhd,atlas_greymatter_reg,atlas_whitematter_reg.mhd>

I get the error:

parameters must already contain an atlas node if you wish to specify atlas volumes..

I cannot understand the --parametersMRMLNodeName in this context. If I don't give atlas paths I get the error:

No default atlas node is available.

Please help.

AM Mohan Rao

On Tue, Mar 16, 2010 at 6:52 PM, Madan Rao <[hidden email] <mailto:[hidden email]>> wrote:

   Hello Steve,

   Thanks. It seems to be working now by following your suggestion.

   However, I cant get the --help running from cmd by:

   Slicer3 --launch EMSegmentCommandLine --help

   Can you explain it?

   AM Mohan Rao



   On Tue, Mar 16, 2010 at 3:31 PM, Steve Pieper
   <[hidden email] <mailto:[hidden email]>> wrote:

       Hi Mohan -

       I'm not sure about the color file issue (perhaps Nicole knows).

       But for the dll issue you should be able to run a command like:

        <path to>/Slicer3.exe --launch EMSegmentCommandLine.exe

       this will set up the paths for you so you don't need to copy
       anything to the system directories.

       Best,
       Steve


       On M/16/10 3:41 AM, Madan Rao wrote:

           Hello all,

           I also tried running the exe after creating the path in
           the error and
           keeping the txt file with no result.

           AM Mohan Rao

           On Tue, Mar 16, 2010 at 1:03 PM, Madan Rao
           <[hidden email] <mailto:[hidden email]>
           <mailto:[hidden email] <mailto:[hidden email]>>> wrote:

              Hello all,

              I am trying to run the Segmentation on
           EMSegmentCommandLine.exe from
              cmd or cygwin on windows vista using the tutorial data.

              I get the following error:

              ERROR: In
                         ..\..\..\Slicer3\Libs\MRML\vtkMRMLColorTableStorageNode.cxx,
           line 255
              vtkMRMLColorTableStorageNode (04C3CE90): ERROR opening
           colour file
              /home/rao/share/FreeSurfer/FreeSurferColorLUT.txt

              I have Slicer3-build using Cygwin. I am able to run the
           --help
              command from the EMSegmentCommndLine.exe after adding
           about 48 *.dll
              files
              to my system32 library.

              Can anyone help please?

              AM Mohan Rao





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           http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
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Re: EMSegmentCommandLine errors

pieper
Administrator
In reply to this post by madanrao
Hi Mohan -

The standard input and output on windows acts funny sometimes so you may
not be seeing the output stream from --help.  I run my cygwin shells in
rxvt, which is a port of xterm and is available from the cygwin setup
program.  Running the commandline in rxvt does give me the output for
--help.

HTH,
-Steve

On M/16/10 9:22 AM, Madan Rao wrote:

> Hello Steve,
>
> Thanks. It seems to be working now by following your suggestion.
>
> However, I cant get the --help running from cmd by:
>
> Slicer3 --launch EMSegmentCommandLine --help
>
> Can you explain it?
>
> AM Mohan Rao
>
>
> On Tue, Mar 16, 2010 at 3:31 PM, Steve Pieper <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi Mohan -
>
>     I'm not sure about the color file issue (perhaps Nicole knows).
>
>     But for the dll issue you should be able to run a command like:
>
>     <path to>/Slicer3.exe --launch EMSegmentCommandLine.exe
>
>     this will set up the paths for you so you don't need to copy
>     anything to the system directories.
>
>     Best,
>     Steve
>
>
>     On M/16/10 3:41 AM, Madan Rao wrote:
>
>         Hello all,
>
>         I also tried running the exe after creating the path in the
>         error and
>         keeping the txt file with no result.
>
>         AM Mohan Rao
>
>         On Tue, Mar 16, 2010 at 1:03 PM, Madan Rao <[hidden email]
>         <mailto:[hidden email]>
>         <mailto:[hidden email] <mailto:[hidden email]>>> wrote:
>
>             Hello all,
>
>             I am trying to run the Segmentation on
>         EMSegmentCommandLine.exe from
>             cmd or cygwin on windows vista using the tutorial data.
>
>             I get the following error:
>
>             ERROR: In
>             ..\..\..\Slicer3\Libs\MRML\vtkMRMLColorTableStorageNode.cxx,
>         line 255
>             vtkMRMLColorTableStorageNode (04C3CE90): ERROR opening
>         colour file
>             /home/rao/share/FreeSurfer/FreeSurferColorLUT.txt
>
>             I have Slicer3-build using Cygwin. I am able to run the --help
>             command from the EMSegmentCommndLine.exe after adding about
>         48 *.dll
>             files
>             to my system32 library.
>
>             Can anyone help please?
>
>             AM Mohan Rao
>
>
>
>
>
>         _______________________________________________
>         slicer-users mailing list
>         [hidden email] <mailto:[hidden email]>
>         http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>         To unsubscribe: send email to
>         [hidden email]
>         <mailto:[hidden email]> with
>         unsubscribe as the subject
>
>
>
>
> _______________________________________________
> 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: EMSegmentCommandLine errors

Aucoin, Nicole
There's also the Slicer3 command line option  
--no_module_stream_redirect that might help.

Nicole

Steve Pieper wrote:

> Hi Mohan -
>
> The standard input and output on windows acts funny sometimes so you may
> not be seeing the output stream from --help.  I run my cygwin shells in
> rxvt, which is a port of xterm and is available from the cygwin setup
> program.  Running the commandline in rxvt does give me the output for
> --help.
>
> HTH,
> -Steve
>
> On M/16/10 9:22 AM, Madan Rao wrote:
>  
>> Hello Steve,
>>
>> Thanks. It seems to be working now by following your suggestion.
>>
>> However, I cant get the --help running from cmd by:
>>
>> Slicer3 --launch EMSegmentCommandLine --help
>>
>> Can you explain it?
>>
>> AM Mohan Rao
>>
>>
>> On Tue, Mar 16, 2010 at 3:31 PM, Steve Pieper <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>>     Hi Mohan -
>>
>>     I'm not sure about the color file issue (perhaps Nicole knows).
>>
>>     But for the dll issue you should be able to run a command like:
>>
>>     <path to>/Slicer3.exe --launch EMSegmentCommandLine.exe
>>
>>     this will set up the paths for you so you don't need to copy
>>     anything to the system directories.
>>
>>     Best,
>>     Steve
>>
>>
>>     On M/16/10 3:41 AM, Madan Rao wrote:
>>
>>         Hello all,
>>
>>         I also tried running the exe after creating the path in the
>>         error and
>>         keeping the txt file with no result.
>>
>>         AM Mohan Rao
>>
>>         On Tue, Mar 16, 2010 at 1:03 PM, Madan Rao <[hidden email]
>>         <mailto:[hidden email]>
>>         <mailto:[hidden email] <mailto:[hidden email]>>> wrote:
>>
>>             Hello all,
>>
>>             I am trying to run the Segmentation on
>>         EMSegmentCommandLine.exe from
>>             cmd or cygwin on windows vista using the tutorial data.
>>
>>             I get the following error:
>>
>>             ERROR: In
>>             ..\..\..\Slicer3\Libs\MRML\vtkMRMLColorTableStorageNode.cxx,
>>         line 255
>>             vtkMRMLColorTableStorageNode (04C3CE90): ERROR opening
>>         colour file
>>             /home/rao/share/FreeSurfer/FreeSurferColorLUT.txt
>>
>>             I have Slicer3-build using Cygwin. I am able to run the --help
>>             command from the EMSegmentCommndLine.exe after adding about
>>         48 *.dll
>>             files
>>             to my system32 library.
>>
>>             Can anyone help please?
>>
>>             AM Mohan Rao
>>
>>
>>
>>
>>
>>         _______________________________________________
>>         slicer-users mailing list
>>         [hidden email] <mailto:[hidden email]>
>>         http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>>         To unsubscribe: send email to
>>         [hidden email]
>>         <mailto:[hidden email]> with
>>         unsubscribe as the subject
>>
>>
>>
>>
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>> [hidden email]
>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
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Re: EMSegmentCommandLine errors

madanrao
In reply to this post by pieper
Hello Steve,

Thanks.

I have rxvt sh-3.2 which I had installed few years ago as part of my then interest in "Wave Form Data Base", but never got to use it.

I tried several things like --help, -help etc., which give ...command not found response.

How do I get to run  licer3-build --launch EMSegmentCommandLine --help from rxvt?

Could you please suggest a link for using this highly appreciated tool?

AM Mohan Rao

On Tue, Mar 16, 2010 at 10:24 PM, Steve Pieper <[hidden email]> wrote:
Hi Mohan -

The standard input and output on windows acts funny sometimes so you may not be seeing the output stream from --help.  I run my cygwin shells in rxvt, which is a port of xterm and is available from the cygwin setup program.  Running the commandline in rxvt does give me the output for --help.

HTH,
-Steve


On M/16/10 9:22 AM, Madan Rao wrote:
Hello Steve,

Thanks. It seems to be working now by following your suggestion.

However, I cant get the --help running from cmd by:

Slicer3 --launch EMSegmentCommandLine --help

Can you explain it?

AM Mohan Rao


On Tue, Mar 16, 2010 at 3:31 PM, Steve Pieper <[hidden email]
<mailto:[hidden email]>> wrote:

   Hi Mohan -

   I'm not sure about the color file issue (perhaps Nicole knows).

   But for the dll issue you should be able to run a command like:

   <path to>/Slicer3.exe --launch EMSegmentCommandLine.exe

   this will set up the paths for you so you don't need to copy
   anything to the system directories.

   Best,
   Steve


   On M/16/10 3:41 AM, Madan Rao wrote:

       Hello all,

       I also tried running the exe after creating the path in the
       error and
       keeping the txt file with no result.

       AM Mohan Rao

       On Tue, Mar 16, 2010 at 1:03 PM, Madan Rao <[hidden email]
       <mailto:[hidden email]>
       <mailto:[hidden email] <mailto:[hidden email]>>> wrote:

           Hello all,

           I am trying to run the Segmentation on
       EMSegmentCommandLine.exe from
           cmd or cygwin on windows vista using the tutorial data.

           I get the following error:

           ERROR: In
           ..\..\..\Slicer3\Libs\MRML\vtkMRMLColorTableStorageNode.cxx,
       line 255
           vtkMRMLColorTableStorageNode (04C3CE90): ERROR opening
       colour file
           /home/rao/share/FreeSurfer/FreeSurferColorLUT.txt

           I have Slicer3-build using Cygwin. I am able to run the --help
           command from the EMSegmentCommndLine.exe after adding about
       48 *.dll
           files
           to my system32 library.

           Can anyone help please?

           AM Mohan Rao





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Re: EMSegmentCommandLine errors

pieper
Administrator
Hi Madan -

Maybe it's the way the rxvt is launched - I used a modified cygwin.bat
file that invokes rxvt.  Maybe that makes a difference?

$ cat /c/cygwin/Cygwin.bat
@echo off
C:
chdir C:\cygwin\bin
rxvt -fn courier -e /bin/bash --login -i

 From there I get the help message when I launch the segmenter command line.

HTH,
-Steve


On M/16/10 1:55 PM, Madan Rao wrote:

> Hello Steve,
>
> Thanks.
>
> I have rxvt sh-3.2 which I had installed few years ago as part of my
> then interest in "Wave Form Data Base", but never got to use it.
>
> I tried several things like --help, -help etc., which give ...command
> not found response.
>
> How do I get to run  licer3-build --launch EMSegmentCommandLine --help
> from rxvt?
>
> Could you please suggest a link for using this highly appreciated tool?
>
> AM Mohan Rao
>
> On Tue, Mar 16, 2010 at 10:24 PM, Steve Pieper <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi Mohan -
>
>     The standard input and output on windows acts funny sometimes so you
>     may not be seeing the output stream from --help.  I run my cygwin
>     shells in rxvt, which is a port of xterm and is available from the
>     cygwin setup program.  Running the commandline in rxvt does give me
>     the output for --help.
>
>     HTH,
>     -Steve
>
>
>     On M/16/10 9:22 AM, Madan Rao wrote:
>
>         Hello Steve,
>
>         Thanks. It seems to be working now by following your suggestion.
>
>         However, I cant get the --help running from cmd by:
>
>         Slicer3 --launch EMSegmentCommandLine --help
>
>         Can you explain it?
>
>         AM Mohan Rao
>
>
>         On Tue, Mar 16, 2010 at 3:31 PM, Steve Pieper
>         <[hidden email] <mailto:[hidden email]>
>         <mailto:[hidden email] <mailto:[hidden email]>>>
>         wrote:
>
>             Hi Mohan -
>
>             I'm not sure about the color file issue (perhaps Nicole knows).
>
>             But for the dll issue you should be able to run a command like:
>
>         <path to>/Slicer3.exe --launch EMSegmentCommandLine.exe
>
>             this will set up the paths for you so you don't need to copy
>             anything to the system directories.
>
>             Best,
>             Steve
>
>
>             On M/16/10 3:41 AM, Madan Rao wrote:
>
>                 Hello all,
>
>                 I also tried running the exe after creating the path in the
>                 error and
>                 keeping the txt file with no result.
>
>                 AM Mohan Rao
>
>                 On Tue, Mar 16, 2010 at 1:03 PM, Madan Rao
>         <[hidden email] <mailto:[hidden email]>
>         <mailto:[hidden email] <mailto:[hidden email]>>
>         <mailto:[hidden email] <mailto:[hidden email]>
>         <mailto:[hidden email] <mailto:[hidden email]>>>> wrote:
>
>                     Hello all,
>
>                     I am trying to run the Segmentation on
>                 EMSegmentCommandLine.exe from
>                     cmd or cygwin on windows vista using the tutorial data.
>
>                     I get the following error:
>
>                     ERROR: In
>
>           ..\..\..\Slicer3\Libs\MRML\vtkMRMLColorTableStorageNode.cxx,
>                 line 255
>                     vtkMRMLColorTableStorageNode (04C3CE90): ERROR opening
>                 colour file
>                     /home/rao/share/FreeSurfer/FreeSurferColorLUT.txt
>
>                     I have Slicer3-build using Cygwin. I am able to run
>         the --help
>                     command from the EMSegmentCommndLine.exe after
>         adding about
>                 48 *.dll
>                     files
>                     to my system32 library.
>
>                     Can anyone help please?
>
>                     AM Mohan Rao
>
>
>
>
>
>                 _______________________________________________
>                 slicer-users mailing list
>         [hidden email]
>         <mailto:[hidden email]>
>         <mailto:[hidden email]
>         <mailto:[hidden email]>>
>
>         http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>                 To unsubscribe: send email to
>         [hidden email]
>         <mailto:[hidden email]>
>         <mailto:[hidden email]
>         <mailto:[hidden email]>> with
>
>                 unsubscribe as the subject
>
>
>
>
>         _______________________________________________
>         slicer-users mailing list
>         [hidden email] <mailto:[hidden email]>
>         http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>         To unsubscribe: send email to
>         [hidden email]
>         <mailto:[hidden email]> with
>         unsubscribe as the subject
>
>
>
>
> _______________________________________________
> 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: EMSegmentCommandLine errors

madanrao
Hello Steve,

Thanks.

The script put in cygwin1.bat works not only for the Slicer3-build in cygwin but also Slicer3 in my Program Files folder.

I need to ignore the errors:
 $ cat commands (which belong to Linux)
 replace cat with type gives syntax error.

AM Mohan Rao



On Wed, Mar 17, 2010 at 1:01 AM, Steve Pieper <[hidden email]> wrote:
Hi Madan -

Maybe it's the way the rxvt is launched - I used a modified cygwin.bat file that invokes rxvt.  Maybe that makes a difference?

$ cat /c/cygwin/Cygwin.bat
@echo off
C:
chdir C:\cygwin\bin
rxvt -fn courier -e /bin/bash --login -i

>From there I get the help message when I launch the segmenter command line.

HTH,
-Steve



On M/16/10 1:55 PM, Madan Rao wrote:
Hello Steve,

Thanks.

I have rxvt sh-3.2 which I had installed few years ago as part of my
then interest in "Wave Form Data Base", but never got to use it.

I tried several things like --help, -help etc., which give ...command
not found response.

How do I get to run  licer3-build --launch EMSegmentCommandLine --help
from rxvt?

Could you please suggest a link for using this highly appreciated tool?

AM Mohan Rao

On Tue, Mar 16, 2010 at 10:24 PM, Steve Pieper <[hidden email]
<mailto:[hidden email]>> wrote:

   Hi Mohan -

   The standard input and output on windows acts funny sometimes so you
   may not be seeing the output stream from --help.  I run my cygwin
   shells in rxvt, which is a port of xterm and is available from the
   cygwin setup program.  Running the commandline in rxvt does give me
   the output for --help.

   HTH,
   -Steve


   On M/16/10 9:22 AM, Madan Rao wrote:

       Hello Steve,

       Thanks. It seems to be working now by following your suggestion.

       However, I cant get the --help running from cmd by:

       Slicer3 --launch EMSegmentCommandLine --help

       Can you explain it?

       AM Mohan Rao


       On Tue, Mar 16, 2010 at 3:31 PM, Steve Pieper
       <[hidden email] <mailto:[hidden email]>
       <mailto:[hidden email] <mailto:[hidden email]>>>

       wrote:

           Hi Mohan -

           I'm not sure about the color file issue (perhaps Nicole knows).

           But for the dll issue you should be able to run a command like:

       <path to>/Slicer3.exe --launch EMSegmentCommandLine.exe

           this will set up the paths for you so you don't need to copy
           anything to the system directories.

           Best,
           Steve


           On M/16/10 3:41 AM, Madan Rao wrote:

               Hello all,

               I also tried running the exe after creating the path in the
               error and
               keeping the txt file with no result.

               AM Mohan Rao

               On Tue, Mar 16, 2010 at 1:03 PM, Madan Rao
       <[hidden email] <mailto:[hidden email]>
       <mailto:[hidden email] <mailto:[hidden email]>>
       <mailto:[hidden email] <mailto:[hidden email]>
       <mailto:[hidden email] <mailto:[hidden email]>>>> wrote:

                   Hello all,

                   I am trying to run the Segmentation on
               EMSegmentCommandLine.exe from
                   cmd or cygwin on windows vista using the tutorial data.

                   I get the following error:

                   ERROR: In

         ..\..\..\Slicer3\Libs\MRML\vtkMRMLColorTableStorageNode.cxx,
               line 255
                   vtkMRMLColorTableStorageNode (04C3CE90): ERROR opening
               colour file
                   /home/rao/share/FreeSurfer/FreeSurferColorLUT.txt

                   I have Slicer3-build using Cygwin. I am able to run
       the --help
                   command from the EMSegmentCommndLine.exe after
       adding about
               48 *.dll
                   files
                   to my system32 library.

                   Can anyone help please?

                   AM Mohan Rao





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Re: EMSegmentCommandLine errors

madanrao
In reply to this post by Aucoin, Nicole
Hello Nicole,

Thanks.

I ran the segmentation CommandLine Module using the example:
EMSegmentTutorialTemplate_ImagesOnly.mrml.

ResultLabelmap:EMtest_label.mhd (an empty mhd file called from result.txt)

targetvolumes: t1.nhdr, t2.nhdr (of old brain atlas),

atlasvolumes:
atlas_background.nhdr
atlas_csf.nhdr
atlas_greymatter.nhdr
atlas_whitematter.nhdr

It runs for some time and ends with the errors which are consistently same.

I am attaching the errors file here.

I ran "processmonitor" of Microsoft and found that it is reading all the files in the mrml and the libraries,
except few (the target_t2, the t1.nhdr, t2.nhdr).

I use MSVista laptop with 3MB. RAM.

Is it sufficient to run EMSegmentCommandLine module?

AM Mohan Rao


On Tue, Mar 16, 2010 at 8:28 PM, Nicole Aucoin <[hidden email]> wrote:
Hello,

I'd strongly suggest running it once from the Slicer GUI, then looking at the Error Log to see the full command line that it passes.
The mrml scene files end in .mrml and contain node tags that will allow slicer to reload the output scene (including volumes).

Nicole

Madan Rao wrote:
Hello,

What is the input for EMSegmentCommandLine atlas data?

If I give:

Slicer3 --launch EMSegmentCommandLine --mrmlSceneFileName <path to EMSegmentTutorialTemplate.mhd>
--resultMRMLSceneFileName <path to segmentation.mhd> --targetVolumeFileNames <path to target_t1_normed.mhd,target_t2_normed.mhd> --atlasVolumeFileNames <path to atlas_background_reg.mhd,atlas_csf_reg.mhd,atlas_greymatter_reg,atlas_whitematter_reg.mhd>

I get the error:

parameters must already contain an atlas node if you wish to specify atlas volumes..

I cannot understand the --parametersMRMLNodeName in this context. If I don't give atlas paths I get the error:

No default atlas node is available.

Please help.

AM Mohan Rao

On Tue, Mar 16, 2010 at 6:52 PM, Madan Rao <[hidden email] <mailto:[hidden email]>> wrote:

   Hello Steve,

   Thanks. It seems to be working now by following your suggestion.

   However, I cant get the --help running from cmd by:

   Slicer3 --launch EMSegmentCommandLine --help

   Can you explain it?

   AM Mohan Rao



   On Tue, Mar 16, 2010 at 3:31 PM, Steve Pieper
   <[hidden email] <mailto:[hidden email]>> wrote:

       Hi Mohan -

       I'm not sure about the color file issue (perhaps Nicole knows).

       But for the dll issue you should be able to run a command like:

        <path to>/Slicer3.exe --launch EMSegmentCommandLine.exe

       this will set up the paths for you so you don't need to copy
       anything to the system directories.

       Best,
       Steve


       On M/16/10 3:41 AM, Madan Rao wrote:

           Hello all,

           I also tried running the exe after creating the path in
           the error and
           keeping the txt file with no result.

           AM Mohan Rao

           On Tue, Mar 16, 2010 at 1:03 PM, Madan Rao
           <[hidden email] <mailto:[hidden email]>
           <mailto:[hidden email] <mailto:[hidden email]>>> wrote:

              Hello all,

              I am trying to run the Segmentation on
           EMSegmentCommandLine.exe from
              cmd or cygwin on windows vista using the tutorial data.

              I get the following error:

              ERROR: In
                         ..\..\..\Slicer3\Libs\MRML\vtkMRMLColorTableStorageNode.cxx,
           line 255
              vtkMRMLColorTableStorageNode (04C3CE90): ERROR opening
           colour file
              /home/rao/share/FreeSurfer/FreeSurferColorLUT.txt

              I have Slicer3-build using Cygwin. I am able to run the
           --help
              command from the EMSegmentCommndLine.exe after adding
           about 48 *.dll
              files
              to my system32 library.

              Can anyone help please?

              AM Mohan Rao





           _______________________________________________
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           [hidden email]
           <mailto:[hidden email]>

           http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
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           [hidden email]
           <mailto:[hidden email]>

           with unsubscribe as the subject



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