# \#binarylabelmap

**URL:** https://discourse.slicer.org/tag/binarylabelmap/73.md

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## [Integration of Mimics-like contouring and edit (magnet + grab) functionality into 3D Slicer for segmentation of CT Lumbar bones](https://discourse.slicer.org/t/integration-of-mimics-like-contouring-and-edit-magnet-grab-functionality-into-3d-slicer-for-segmentation-of-ct-lumbar-bones/46000)

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**Author:** [@Mirza\_Ahmad\_Awais](https://discourse.slicer.org/u/Mirza_Ahmad_Awais)\
**Replies:** 1\
**Last updated:** [January 30, 2026, 6:50pm UTC](https://discourse.slicer.org/t/integration-of-mimics-like-contouring-and-edit-magnet-grab-functionality-into-3d-slicer-for-segmentation-of-ct-lumbar-bones/46000 "2026-01-30T18:50:06Z")

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Hello! I am trying to add contouring and edit contouring functionality into 3D slicer as a replacement to mimics or mimics-like tool so we can accurately segment lumbar bodies for surgical implant design purposes. Firstl…

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## [Converting .stl files to binary label maps in .nii format using Python](https://discourse.slicer.org/t/converting-stl-files-to-binary-label-maps-in-nii-format-using-python/13038)

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**Author:** [@DC-3T](https://discourse.slicer.org/u/DC-3T)\
**Replies:** 11\
**Last updated:** [August 25, 2024, 8:29pm UTC](https://discourse.slicer.org/t/converting-stl-files-to-binary-label-maps-in-nii-format-using-python/13038 "2024-08-25T20:29:43Z")

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Dear all, I hope you’re doing well. I’ve spent the last week or two struggling to convert a large number of .stl files (~1,000) drawn in 3D Slicer 4.10.2 into .nii binary label maps using Python. The .stl data were deri…

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## [Saving transformed Volumes](https://discourse.slicer.org/t/saving-transformed-volumes/1266)

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**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\
**Replies:** 18\
**Last updated:** [January 15, 2024, 8:36am UTC](https://discourse.slicer.org/t/saving-transformed-volumes/1266 "2024-01-15T08:36:21Z")

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Hi, I am trying to save binary labelmaps that I have transformed with specific transform files. The problem is that I have clicked the harden transform button, but when I go to save the files, they do not save in the cor…

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## [Is there a faster way to read and write a segment as a numpy array?](https://discourse.slicer.org/t/is-there-a-faster-way-to-read-and-write-a-segment-as-a-numpy-array/32487)

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**Author:** [@abhilaksh\_singh\_reen](https://discourse.slicer.org/u/abhilaksh_singh_reen)\
**Replies:** 6\
**Last updated:** [November 26, 2023, 12:11pm UTC](https://discourse.slicer.org/t/is-there-a-faster-way-to-read-and-write-a-segment-as-a-numpy-array/32487 "2023-11-26T12:11:40Z")

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Hi. My team is building a Python Scripted Slicer Module for an organ segmentation task. We have a Segmentation Model to which we are only giving a single slice as input (at a time) and the model outputs the mask for tha…

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## [Import Numpy File in as image volume](https://discourse.slicer.org/t/import-numpy-file-in-as-image-volume/3653)

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**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\
**Replies:** 5\
**Last updated:** [December 12, 2022, 10:47pm UTC](https://discourse.slicer.org/t/import-numpy-file-in-as-image-volume/3653 "2022-12-12T22:47:35Z")

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I have been working with trying to compress files down to NPY and NPZ files to save binary labelmaps for some of my data. Is there a way to import them into slicer? Every time I try the load data option with it, it doesn…

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## [How to convert a vtkMRMLScalarVolumeNode to a vtkMRMLSegmentationNode](https://discourse.slicer.org/t/how-to-convert-a-vtkmrmlscalarvolumenode-to-a-vtkmrmlsegmentationnode/20343)

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**Author:** [@kkkkkkk123](https://discourse.slicer.org/u/kkkkkkk123)\
**Replies:** 7\
**Last updated:** [January 21, 2022, 8:06pm UTC](https://discourse.slicer.org/t/how-to-convert-a-vtkmrmlscalarvolumenode-to-a-vtkmrmlsegmentationnode/20343 "2022-01-21T20:06:04Z")

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Hi all, I’m trying to convert a vtkMRMLScalarVolumeNode to a new vtkMRMLSegmentationNode (in Python) and I don’t seem to get it figured out… The scalar volume is basically just a binary image but I want it to be rendere…

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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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## [stl to labelmap does not work for reference volume](https://discourse.slicer.org/t/stl-to-labelmap-does-not-work-for-reference-volume/18248)

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**Author:** [@straj](https://discourse.slicer.org/u/straj)\
**Replies:** 1\
**Last updated:** [June 21, 2021, 1:32pm UTC](https://discourse.slicer.org/t/stl-to-labelmap-does-not-work-for-reference-volume/18248 "2021-06-21T13:32:23Z")

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Hi, I’m currently trying to convert an stl file to a binary labelmap, which seems to work fine as long as I do not choose a reference volume under ‘advanced’. If i do so, the labelmap which is created has the correct sp…

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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?

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## [Adjusting and saving binary labelmaps](https://discourse.slicer.org/t/adjusting-and-saving-binary-labelmaps/1126)

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**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\
**Replies:** 7\
**Last updated:** [June 13, 2018, 7:05pm UTC](https://discourse.slicer.org/t/adjusting-and-saving-binary-labelmaps/1126 "2018-06-13T19:05:36Z")

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I have cropped ROI volumes that were registered and their segmentations transforms and exported to binary labelmaps. I am trying to save those labelmaps to files that have the same dimensions so that I can create a proba…