[slicer-users] EMSegmentCommandLine errors

Nicole Aucoin nicole at bwh.harvard.edu
Tue Mar 16 10:58:23 EDT 2010


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 <rao.lms at gmail.com 
> <mailto:rao.lms at gmail.com>> 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
>     <pieper at bwh.harvard.edu <mailto:pieper at bwh.harvard.edu>> 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
>             <rao.lms at gmail.com <mailto:rao.lms at gmail.com>
>             <mailto:rao.lms at gmail.com <mailto:rao.lms at gmail.com>>> 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
>             slicer-users at bwh.harvard.edu
>             <mailto:slicer-users at bwh.harvard.edu>
>             http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>             To unsubscribe: send email to
>             slicer-users-request at massmail.spl.harvard.edu
>             <mailto:slicer-users-request at massmail.spl.harvard.edu>
>             with unsubscribe as the subject
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> slicer-users mailing list
> slicer-users at bwh.harvard.edu
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to slicer-users-request at massmail.spl.harvard.edu with unsubscribe as the subject




More information about the slicer-users mailing list