# \#labelmap

**URL:** https://discourse.slicer.org/tag/labelmap/130.md

[Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md)

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## [Issues with multiple labels and masks overlapping in Monailabel](https://discourse.slicer.org/t/issues-with-multiple-labels-and-masks-overlapping-in-monailabel/44448)

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**Author:** [@koumeasa](https://discourse.slicer.org/u/koumeasa)\
**Replies:** 1\
**Last updated:** [September 29, 2025, 9:29am UTC](https://discourse.slicer.org/t/issues-with-multiple-labels-and-masks-overlapping-in-monailabel/44448 "2025-09-29T09:29:51Z")

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Hey everyone, I’m labeling brain segments in MONAILabel. The masks / ROIs used as input for Monailabel are a subselection extracted by slicerio.extract\_segments() function from a 3DSlicer Segmentation node. I modified …

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## [Labelmap combine issue](https://discourse.slicer.org/t/labelmap-combine-issue/34171)

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**Author:** [@Hobart10](https://discourse.slicer.org/u/Hobart10)\
**Replies:** 0\
**Last updated:** [February 6, 2024, 3:23pm UTC](https://discourse.slicer.org/t/labelmap-combine-issue/34171 "2024-02-06T15:23:55Z")

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Hi, there are two labelmap volumes from same source brain atlas that I would like to combine to one for further registration, but they are both having sequential digital labels and I hope to not overwrite in ‘Image label…

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## [Preserve colors from segment editor node and export it as Nifti LabelMap](https://discourse.slicer.org/t/preserve-colors-from-segment-editor-node-and-export-it-as-nifti-labelmap/33100)

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**Author:** [@Vishal\_P](https://discourse.slicer.org/u/Vishal_P)\
**Replies:** 8\
**Last updated:** [December 1, 2023, 2:11am UTC](https://discourse.slicer.org/t/preserve-colors-from-segment-editor-node-and-export-it-as-nifti-labelmap/33100 "2023-12-01T02:11:02Z")

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Slicer 5.2.2 Hello, i am currently using segment editor and selected Generic Color Table and made following sample segments. and then i move the segments to segmentation module and export it as a new label map, once…

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## [Unable to create LabelMaps for ModelMaker](https://discourse.slicer.org/t/unable-to-create-labelmaps-for-modelmaker/32163)

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**Author:** [@BlancaRodriguez](https://discourse.slicer.org/u/BlancaRodriguez)\
**Replies:** 1\
**Last updated:** [October 11, 2023, 5:56pm UTC](https://discourse.slicer.org/t/unable-to-create-labelmaps-for-modelmaker/32163 "2023-10-11T17:56:46Z")

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Hello! My team and I are currently working in a segmentation project, and have been actively using Slicer. However, we are currently facing some challenges and hope we can get some help from the community. Specifically…

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## [LabelOverlay Image saved as DICOM series](https://discourse.slicer.org/t/labeloverlay-image-saved-as-dicom-series/27725)

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**Author:** [@Franciska](https://discourse.slicer.org/u/Franciska)\
**Replies:** 8\
**Last updated:** [February 14, 2023, 8:59pm UTC](https://discourse.slicer.org/t/labeloverlay-image-saved-as-dicom-series/27725 "2023-02-14T20:59:19Z")

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Hi! I have a DICOM series, and with the segmentations I create a LabelOverlay Image. When I write it out as a DICOM series, I modified the following datatags in the created image, to get an RGB image.: image\_slice.Se…

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## [Tranformation of labelmap not working on script](https://discourse.slicer.org/t/tranformation-of-labelmap-not-working-on-script/25499)

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**Author:** [@justomont](https://discourse.slicer.org/u/justomont)\
**Replies:** 8\
**Last updated:** [October 19, 2022, 6:35am UTC](https://discourse.slicer.org/t/tranformation-of-labelmap-not-working-on-script/25499 "2022-10-19T06:35:21Z")

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Operating system: MacOS BigSur 11.6 Slicer version: 5.0.3 Expected behavior: Transform labelmap volume node Actual behavior: Labelmap volume node is not transformed Hello everyone, I’m developing a script, that amon…

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## [Importing label maps with MultiVolumeImporter as segmentations](https://discourse.slicer.org/t/importing-label-maps-with-multivolumeimporter-as-segmentations/24458)

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**Author:** [@pitfall24](https://discourse.slicer.org/u/pitfall24)\
**Replies:** 1\
**Last updated:** [July 23, 2022, 5:53am UTC](https://discourse.slicer.org/t/importing-label-maps-with-multivolumeimporter-as-segmentations/24458 "2022-07-23T05:53:19Z")

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I have a series of nifti files which form a 4D sequence. Using MultiVolumeImporter/Explorer I was able to view the volumes perfectly. However I also have a series of corresponding segmentations in the same nifti format w…

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## [Labelmap volume rendering preset (default) is not available from preset dropdown](https://discourse.slicer.org/t/labelmap-volume-rendering-preset-default-is-not-available-from-preset-dropdown/20375)

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**Author:** [@DIV](https://discourse.slicer.org/u/DIV)\
**Replies:** 8\
**Last updated:** [October 29, 2021, 4:52am UTC](https://discourse.slicer.org/t/labelmap-volume-rendering-preset-default-is-not-available-from-preset-dropdown/20375 "2021-10-29T04:52:10Z")

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If I create a volume from the Simple Region Growing Segmentation module, then I suppose it is a binary labelmap. It can be viewed in 3D through the Volume Rendering module. By default this comes up with a kind of colo…

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## [Label image defects after saving](https://discourse.slicer.org/t/label-image-defects-after-saving/20062)

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**Author:** [@MachadoL](https://discourse.slicer.org/u/MachadoL)\
**Replies:** 3\
**Last updated:** [October 8, 2021, 2:02pm UTC](https://discourse.slicer.org/t/label-image-defects-after-saving/20062 "2021-10-08T14:02:38Z")

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Guys, I am not sure if that is the correct place to ask that, BUT I have nowhere to run. I used nrrd and slicerio extensions to separate .seg.nrrd files into separated segments or label images. Great. It gives me array…

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## [Help with binary labelmaps of reformatted DICOM ](https://discourse.slicer.org/t/help-with-binary-labelmaps-of-reformatted-dicom/18485)

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**Author:** [@DaZo](https://discourse.slicer.org/u/DaZo)\
**Replies:** 1\
**Last updated:** [July 8, 2021, 5:29pm UTC](https://discourse.slicer.org/t/help-with-binary-labelmaps-of-reformatted-dicom/18485 "2021-07-08T17:29:11Z")

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Operating system: Win 10 Home Slicer version: 4.10.2 Expected behavior: Actual behavior: Hi everyone! I have the following issue: I want to create a 2D segmentation on a single slice of reformatted CT DICOM images a…

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## [Issue with Mesh to Label Map](https://discourse.slicer.org/t/issue-with-mesh-to-label-map/17875)

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**Author:** [@quan](https://discourse.slicer.org/u/quan)\
**Replies:** 2\
**Last updated:** [June 1, 2021, 5:18am UTC](https://discourse.slicer.org/t/issue-with-mesh-to-label-map/17875 "2021-06-01T05:18:30Z")

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I’m trying to generate a SPHARM-PDM mesh from a .stl file. I imported the .stl and used “Mesh to Label Map” to obtain the .nrrd. However, the .nrrd is inverted (the white space are supposed to be black and vice versa). T…

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## [Volume rendering of binary label maps](https://discourse.slicer.org/t/volume-rendering-of-binary-label-maps/4411)

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**Author:** [@katharina\_hecker](https://discourse.slicer.org/u/katharina_hecker)\
**Replies:** 10\
**Last updated:** [February 8, 2021, 6:53pm UTC](https://discourse.slicer.org/t/volume-rendering-of-binary-label-maps/4411 "2021-02-08T18:53:42Z")

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Hello everyone, is it generally possible to use the volume rendering module for created binary label maps, which were originating from segmentations? I was exporting my segments to binary label maps and were trying to …

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## [Read Dicom label map and export .nrrd label map](https://discourse.slicer.org/t/read-dicom-label-map-and-export-nrrd-label-map/15627)

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**Author:** [@diehumblex](https://discourse.slicer.org/u/diehumblex)\
**Replies:** 3\
**Last updated:** [January 23, 2021, 9:53pm UTC](https://discourse.slicer.org/t/read-dicom-label-map-and-export-nrrd-label-map/15627 "2021-01-23T21:53:46Z")

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Hi! i am trying to convert dicom label map into nrrd. on save only option i get is mrd mrml and seg.vtm Any help would be appreciated. Thank you. About Dataset: I am using HN1 dataset for this. Each patient contains 3 …

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## [Call an specifica class frome c++ in python](https://discourse.slicer.org/t/call-an-specifica-class-frome-c-in-python/13777)

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**Author:** [@aldoSanchez](https://discourse.slicer.org/u/aldoSanchez)\
**Replies:** 2\
**Last updated:** [September 30, 2020, 5:05pm UTC](https://discourse.slicer.org/t/call-an-specifica-class-frome-c-in-python/13777 "2020-09-30T17:05:41Z")

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hello I’m trying to access to this action: vtkMRMLLabelMapVolumeDisplayNode::vtkMRMLLabelMapVolumeDisplayNode() { this-\>MapToColors = vtkImageMapToColors::New(); this-\>MapToColors-\>SetOutputFormatToRGBA(); // set …

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## [Is it possible to merge multiple labels into one label in a segmentation image?](https://discourse.slicer.org/t/is-it-possible-to-merge-multiple-labels-into-one-label-in-a-segmentation-image/13764)

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**Author:** [@kevin.x](https://discourse.slicer.org/u/kevin.x)\
**Replies:** 1\
**Last updated:** [September 30, 2020, 9:18am UTC](https://discourse.slicer.org/t/is-it-possible-to-merge-multiple-labels-into-one-label-in-a-segmentation-image/13764 "2020-09-30T09:18:04Z")

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Hi all, I have an image with multiple labels and I want to merge them and label it as a single label. Is it possible for me to do it in 3D Slicer or ITK-SNAP? Here is the image displaying in 3D Slicer and ITK-SNAP: …

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## [Trouble generating Labelmap from segmentation](https://discourse.slicer.org/t/trouble-generating-labelmap-from-segmentation/10951)

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**Author:** [@Maxibers](https://discourse.slicer.org/u/Maxibers)\
**Replies:** 3\
**Last updated:** [April 3, 2020, 5:32pm UTC](https://discourse.slicer.org/t/trouble-generating-labelmap-from-segmentation/10951 "2020-04-03T17:32:02Z")

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Good morning, my goal is to automatically load segmentations and save them in a labelmap format, but i’m having trouble: When i create the labelmap manually (from the segment editor module), save it manually and load i…

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## [Importing labeled image to segment directly](https://discourse.slicer.org/t/importing-labeled-image-to-segment-directly/10597)

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**Author:** [@muntahi398](https://discourse.slicer.org/u/muntahi398)\
**Replies:** 2\
**Last updated:** [March 9, 2020, 6:23pm UTC](https://discourse.slicer.org/t/importing-labeled-image-to-segment-directly/10597 "2020-03-09T18:23:32Z")

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Dear slicer experts, Recently I was working with some 3D image volume analysis in another software. Then I am trying to further analyze and visualize the volume in 3d slicer. work step Import volume of segemented and…

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## [Automatically view LabelMapNodes](https://discourse.slicer.org/t/automatically-view-labelmapnodes/10036)

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**Author:** [@kleingeo](https://discourse.slicer.org/u/kleingeo)\
**Replies:** 7\
**Last updated:** [January 31, 2020, 5:51pm UTC](https://discourse.slicer.org/t/automatically-view-labelmapnodes/10036 "2020-01-31T17:51:04Z")

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I developed a segmentation module and want to be able to display the segmentation after it is generated, but I am unsure how to do it. This is what I have so far (for the relevant parts). Any help would be much appreciat…

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## [Transfer 3D Slicer segmentations to Avizo](https://discourse.slicer.org/t/transfer-3d-slicer-segmentations-to-avizo/6837)

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**Author:** [@dekaya](https://discourse.slicer.org/u/dekaya)\
**Replies:** 3\
**Last updated:** [May 21, 2019, 1:44am UTC](https://discourse.slicer.org/t/transfer-3d-slicer-segmentations-to-avizo/6837 "2019-05-21T01:44:31Z")

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Hi everyone, I have been working on segmenting micro CT data for a palaeontology specimen in 3D slicer. The files have been saved as MRB containing: .nrrd .seg.nrrd .vp .acsv (annotationROI) In total, I have 9 diff…

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## [Drawing Polygons on Labelmap Masks](https://discourse.slicer.org/t/drawing-polygons-on-labelmap-masks/5994)

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**Author:** [@gleman](https://discourse.slicer.org/u/gleman)\
**Replies:** 2\
**Last updated:** [March 7, 2019, 3:52am UTC](https://discourse.slicer.org/t/drawing-polygons-on-labelmap-masks/5994 "2019-03-07T03:52:37Z")

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I’ve got a function that produces a list of vtkPolygons (that I put together into a vtkPolyData) that I’d like to “draw” on a labelmap mask. It looks like EditorLib.LabelEffect.slicer.SegmentEditorDrawEffect.scriptedEf…

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## [Resampling a Labelmap Volume](https://discourse.slicer.org/t/resampling-a-labelmap-volume/5545)

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**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\
**Replies:** 2\
**Last updated:** [January 29, 2019, 1:48am UTC](https://discourse.slicer.org/t/resampling-a-labelmap-volume/5545 "2019-01-29T01:48:41Z")

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How can I resample a binary labelmap volume to an image origin of \[0,0,0\] and an image spacing of \[1,1,1\] that preserves the labelmap classes in the volume output? Is there a way to do this programmatically?