https://www.slicer.org/w/index.php?action=history&feed=atom&title=Modules%3AEM-Segmenter-Documentation%3ACommandLineInterfaceModules:EM-Segmenter-Documentation:CommandLineInterface - Revision history2026-05-04T05:57:33ZRevision history for this page on the wikiMediaWiki 1.33.0https://www.slicer.org/w/index.php?title=Modules:EM-Segmenter-Documentation:CommandLineInterface&diff=4974&oldid=prevDavisb: New page: USAGE: ./EMSegmentCommandLine [--processinformationaddress <std::string>] [--xml] [--echo] [--disableCompression] [--resultMRMLS...2008-05-28T13:43:48Z<p>New page: USAGE: ./EMSegmentCommandLine [--processinformationaddress <std::string>] [--xml] [--echo] [--disableCompression] [--resultMRMLS...</p>
<p><b>New page</b></p><div>USAGE: <br />
<br />
./EMSegmentCommandLine [--processinformationaddress <std::string>]<br />
[--xml] [--echo] [--disableCompression]<br />
[--resultMRMLSceneFileName <std::string>]<br />
[--generateEmptyMRMLSceneAndQuit <std::string>]<br />
[--dontWriteResults]<br />
[--resultStandardVolumeFileName <std::string>]<br />
[--verbose] [--dontUpdateIntermediateData]<br />
[--disableMultithreading]<br />
[--parametersMRMLNodeName <std::string>]<br />
[--intermediateResultsDirectory <std::string>]<br />
[--atlasVolumeFileNames<br />
<std::vector<std::string>>] ... <br />
[--targetVolumeFileNames<br />
<std::vector<std::string>>] ... <br />
[--resultVolumeFileName <std::string>]<br />
[--mrmlSceneFileName <std::string>] [--]<br />
[--version] [-h]<br />
<br />
<br />
Where: <br />
<br />
--processinformationaddress <std::string><br />
Address of a structure to store process information (progress, abort,<br />
etc.). (default: 0)<br />
<br />
--xml<br />
Produce xml description of command line arguments (default: 0)<br />
<br />
--echo<br />
Echo the command line arguments (default: 0)<br />
<br />
--disableCompression<br />
Don't use compression when writing result image to disk. (default: 0)<br />
<br />
--resultMRMLSceneFileName <std::string><br />
Write out the MRML scene after command line substitutions have been<br />
made.<br />
<br />
--generateEmptyMRMLSceneAndQuit <std::string><br />
Used for testing. Only write a scene with default mrml parameters.<br />
<br />
--dontWriteResults<br />
Used for testing. Don't actually write the resulting labelmap to<br />
disk. (default: 0)<br />
<br />
--resultStandardVolumeFileName <std::string><br />
Used for testing. Compare segmentation results to this image and<br />
return EXIT_FAILURE if they do not match.<br />
<br />
--verbose<br />
Enable verbose output. (default: 0)<br />
<br />
--dontUpdateIntermediateData<br />
Disable update of intermediate results. (default: 0)<br />
<br />
--disableMultithreading<br />
Disable multithreading. (default: 0)<br />
<br />
--parametersMRMLNodeName <std::string><br />
The name of the EMSegment parameters node within the active MRML<br />
scene. Leave blank for default.<br />
<br />
--intermediateResultsDirectory <std::string><br />
Directory where EMSegmenter will write intermediate data (e.g.,<br />
aligned atlas data).<br />
<br />
--atlasVolumeFileNames <std::vector<std::string>> (accepted multiple<br />
times)<br />
File names of atlas (spatial) probability maps. The number of atlas<br />
volumes must match the number specified in the parameter set. The<br />
ordering must match the ordering defined in the mrml parameters file.<br />
<br />
--targetVolumeFileNames <std::vector<std::string>> (accepted multiple<br />
times)<br />
File names of target volumes (to be segmented). The number of target<br />
images must be equal to the number of target images specified in the<br />
parameter set, and these images must be spatially aligned.<br />
<br />
--resultVolumeFileName <std::string><br />
The file name that the segmentation result volume will be written to.<br />
<br />
--mrmlSceneFileName <std::string><br />
Active MRML scene that contains EMSegment algorithm parameters.<br />
<br />
--, --ignore_rest<br />
Ignores the rest of the labeled arguments following this flag.<br />
<br />
--version<br />
Displays version information and exits.<br />
<br />
-h, --help<br />
Displays usage information and exits.<br />
<br />
<br />
Description: EMSegment command-line module description and<br />
help.<br />
<br />
Author(s): Brad Davis<br />
<br />
Acknowledgements: Many people and organizations have contributed to the<br />
funding, design, and development of the EMSegment algorithm and its<br />
various implementations.</div>Davisb