Units of extent in DetermineCommonLabelmapExtent

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Units of extent in DetermineCommonLabelmapExtent

Dzenan Zukic
Hi everybody,

what are the units of extent in vtkSegmentation::DetermineCommonLabelmapExtent()? Index units of base image, index units of label map, rounded physical units?

Or to rephrase the question: what is the easiest way to calculate origin+size for cropping the base image to just the non-background part of the label map (vtkSegmentation)? I was planning to invoke ResampleScalarVectorDWIVolume.

Thanks,
Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

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Re: Units of extent in DetermineCommonLabelmapExtent

lasso2

If you need segmentation results as labelmap in a particular geometry (e.g., matching geometry of an existing volume), then in Segmentations module “Export/import segments” section choose Export, Labelmap, and in Advanced section select a Reference volume.

 

DetermineCommonLabelmapExtent returns a standard vtkImageData extent for the common image geometry (origin, spacing, axis directions) for all labelmaps in the segmentation. To get origin, spacing, axis directions, and extents for all labelmaps, use DetermineCommonLabelmapGeometry:

https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Core/vtkMRMLSegmentationStorageNode.cxx#L934..L936

 

There is no such thing as a “base image” for a segmentation node. For segmentation editing you must choose a master volume, but that’s just an editing setting, the volume is not associated with the segmentation node.

 

Andras

 

From: slicer-devel [mailto:[hidden email]] On Behalf Of Dzenan Zukic
Sent: March 13, 2017 17:41
To: SPL Slicer Devel <[hidden email]>
Subject: [slicer-devel] Units of extent in DetermineCommonLabelmapExtent

 

Hi everybody,

 

what are the units of extent in vtkSegmentation::DetermineCommonLabelmapExtent()? Index units of base image, index units of label map, rounded physical units?

 

Or to rephrase the question: what is the easiest way to calculate origin+size for cropping the base image to just the non-background part of the label map (vtkSegmentation)? I was planning to invoke ResampleScalarVectorDWIVolume.

 

Thanks,

Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)


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