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IDProjectCategoryView StatusLast Update
0004400Slicer4Core: Segmentationpublic2018-08-28 11:04
ReporterpinterAssigned Topinter 
PrioritynormalSeveritymajorReproducibilityN/A
Status assignedResolutionopen 
Product VersionSlicer 4.7.0 
Target VersionSlicer 4.11.0Fixed in Version 
Summary0004400: Support Segmentation nodes in CLI modules
Description

CLI modules are simpler to implement but the CLI interface does not support all node types. The Slicer core should be enhanced to allow passing of Segmentation nodes.

Segmentations can provide both labelmap or geometry output. So, the idea would be to allow selecting segmentation node for <image type="label"> (in addition to vtkMRMLLabelMapVolumeNode) and for <geometry type="model"> (in addition to vtkMRMLModelNode). This would allow using CLI modules with segmentations without any changes.

We would add a new type for overlapping labels (<image type="overlapping-label">), which would pass a 4D NRRD file.

Additional Information

Moved here from SlicerRT because Segmentations is now in Slicer core
https://app.assembla.com/spaces/slicerrt/tickets/165-allow-slicer-to-pass-segmentation-nodes-to-cli-modules/details

TagsNo tags attached.

Activities

jcfr

jcfr

2018-03-22 01:28

administrator   ~0015593

Last edited: 2018-03-22 01:29

View 3 revisions

@pinter: Since this is a significant endeavor, I re-targeted to Slicer 5.0. If you plan to work on this in the coming days, do not hesitate to set the target back.

pinter

pinter

2018-03-22 08:20

developer   ~0015606

Last edited: 2018-03-22 08:22

View 2 revisions

Definitely. Thanks!

Actually we don't have much motivation to get this done in the near future. We don't use CLIs, and we haven't got any questions about this either. If there was public interest, I'd work on this, but otherwise this is only a nice-to-have for us.

lassoan

lassoan

2018-08-28 11:04

developer   ~0015981

How to implement segmentation node input for CLI modules:

To support overlapping labels (stored in 4D volumes), a new image type could be added. Current labelmap node type name is "label". Name of the new type could be "overlapping-label" or "multi-label". This would be written as 4D nrrd, each label as a 3D frame.

Similar changes are needed to allow CLIs to have segmentation node output.

Issue History

Date Modified Username Field Change
2017-07-25 14:27 pinter New Issue
2017-07-25 14:27 pinter Status new => assigned
2017-07-25 14:27 pinter Assigned To => pinter
2017-10-18 01:18 jcfr Target Version Slicer 4.8.1 => Slicer 4.9.0
2018-03-22 01:28 jcfr Note Added: 0015593
2018-03-22 01:28 jcfr Target Version Slicer 4.9.0 => Slicer 4.11.0
2018-03-22 01:29 jcfr Note Edited: 0015593 View Revisions
2018-03-22 01:29 jcfr Note Edited: 0015593 View Revisions
2018-03-22 08:20 pinter Note Added: 0015606
2018-03-22 08:22 pinter Note Edited: 0015606 View Revisions
2018-08-28 11:04 lassoan Note Added: 0015981