EMSegmenter Command Line Interface

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EMSegmenter Command Line Interface

Yu,Justin
Hi all,

I have a large number of brain MRI cases that I need to auto-segment in white matter, grey matter, and CSF. So far, I have been working with the EMSegment Module.

The module seems to be working fine, but I plan to script the auto-segmentation process to save time, and I have been trying to use the EMSegmenter Command Line Interface (CLI). However, I'm not sure which inputs are required and which are optional. Can someone please give me the details about how to use the EMSegmenter CLI?

Thanks,
Justin

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Re: EMSegmenter Command Line Interface

Kilian Pohl
Hi Justin,

Have you read through

http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Overview

The bare minimum is the mrml file defining the emsegment parameters, e.g.

/software/Slicer4/superbuild/Slicer-build/Slicer --launcher-no-splash --launch /software/Slicer4/superbuild/Slicer-build/lib/Slicer-4.2/cli-modules/EMSegmentCommandLine --mrmlSceneFileName /software/Slicer3/Slicer3/Modules/EMSegment/Testing/TestData/TutorialTest/Template_small.mrml

If you want to run it in batch mode it normally makes sense to also define a different image file to segmentation then the one in the mrml file

--targetVolumeFileNames /software/Slicer3/Slicer3/Modules/EMSegment/Testing/TestData/TutorialTest/VolumeData/targetT1Normed_small.mhd

if you furthermore want to specify the name of the final segmentation then you can do that by adding the following option to the command above

--resultVolumeFileName /software/Slicer4/superbuild/Slicer-build/Modules/Remote/EMSegment/EMSegCL_RunDefaultNodes_tmp.mhd


Hope it helps

Kilian

Ps : if the EMSegmenter is part of your machinery for publishing papers do not forget to cite the paper listed at
http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Overview

thanks :)




On 08/09/2013 12:08 PM, Yu,Justin wrote:
Hi all,

I have a large number of brain MRI cases that I need to auto-segment in white matter, grey matter, and CSF. So far, I have been working with the EMSegment Module.

The module seems to be working fine, but I plan to script the auto-segmentation process to save time, and I have been trying to use the EMSegmenter Command Line Interface (CLI). However, I'm not sure which inputs are required and which are optional. Can someone please give me the details about how to use the EMSegmenter CLI?

Thanks,
Justin


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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/4.2/FAQ


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