# \#masking

**URL:** https://discourse.slicer.org/tag/masking/211.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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## [Fill in part of segment without adding whole model ](https://discourse.slicer.org/t/fill-in-part-of-segment-without-adding-whole-model/47045)

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**Author:** [@akelly17](https://discourse.slicer.org/u/akelly17)\
**Replies:** 1\
**Last updated:** [May 15, 2026, 3:38pm UTC](https://discourse.slicer.org/t/fill-in-part-of-segment-without-adding-whole-model/47045 "2026-05-15T15:38:59Z")

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Hey all, I cannot seem to figure out how to get this section of my model to fill in (i.e: make the segment whole) without adding back the entire model. I have just figured out how the “masking” function works, and am sti…

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## [Odd behavior after adding a moving mask in the ANTs extension](https://discourse.slicer.org/t/odd-behavior-after-adding-a-moving-mask-in-the-ants-extension/46117)

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**Author:** [@sulli419](https://discourse.slicer.org/u/sulli419)\
**Replies:** 9\
**Last updated:** [March 4, 2026, 5:52pm UTC](https://discourse.slicer.org/t/odd-behavior-after-adding-a-moving-mask-in-the-ants-extension/46117 "2026-03-04T17:52:15Z")

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I’ve been using the ANTs extension for registering two single-label volumes to eachother with good results. In an attempt to improve registration robustness, I started incorporating fixed and moving masks (FM, MM), but …

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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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## [SlicerMorph Photogrammetry photo masking issue](https://discourse.slicer.org/t/slicermorph-photogrammetry-photo-masking-issue/43369)

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**Author:** [@chz31](https://discourse.slicer.org/u/chz31)\
**Replies:** 14\
**Last updated:** [June 16, 2025, 11:47pm UTC](https://discourse.slicer.org/t/slicermorph-photogrammetry-photo-masking-issue/43369 "2025-06-16T23:47:30Z")

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I am trying the Slicer Photogrammetry with a student. The photos were taken by a cell phone at a single perspective. However, the masking behaved very weirdly. I’m also not very sure about the orientations. The pho…

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## [Why did the segment created by threshold masking contain voxels beyond the threshold?](https://discourse.slicer.org/t/why-did-the-segment-created-by-threshold-masking-contain-voxels-beyond-the-threshold/40123)

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**Author:** [@qmsyylsel](https://discourse.slicer.org/u/qmsyylsel)\
**Replies:** 4\
**Last updated:** [November 15, 2024, 2:32pm UTC](https://discourse.slicer.org/t/why-did-the-segment-created-by-threshold-masking-contain-voxels-beyond-the-threshold/40123 "2024-11-15T14:32:33Z")

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As the pictures shows, in Segment Editor, I painted my segment under the masking with a threshold of \>130. But in Segment Statistics, the minimum value of that segment was 85, which was lower than 130, the threshold I se…

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## [Elastix masking registration](https://discourse.slicer.org/t/elastix-masking-registration/8039)

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**Author:** [@labixin](https://discourse.slicer.org/u/labixin)\
**Replies:** 12\
**Last updated:** [October 25, 2024, 2:51pm UTC](https://discourse.slicer.org/t/elastix-masking-registration/8039 "2024-10-25T14:51:56Z")

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Hi all, I am using Elastix to register two breast CTs. I have cropped volume to proper size and built masks to each volume. But the registration still failed indicating that “Description: itk::ERROR: AdvancedMattesMutua…

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## [How to create a brain mask from MRI T2 (30 MRI total)](https://discourse.slicer.org/t/how-to-create-a-brain-mask-from-mri-t2-30-mri-total/38338)

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**Author:** [@jegiron](https://discourse.slicer.org/u/jegiron)\
**Replies:** 3\
**Last updated:** [September 13, 2024, 7:36pm UTC](https://discourse.slicer.org/t/how-to-create-a-brain-mask-from-mri-t2-30-mri-total/38338 "2024-09-13T19:36:55Z")

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I have MRI T2 weighed images and need to create a mask to remove skull and others. I have a total of 30 MRI models and need ultimately need to measure infarct volume percentage. I also need to do spatial normalization. H…

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## [Masking/segmentations disappearing issue](https://discourse.slicer.org/t/masking-segmentations-disappearing-issue/33500)

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**Author:** [@ndelgado](https://discourse.slicer.org/u/ndelgado)\
**Replies:** 1\
**Last updated:** [December 22, 2023, 8:15pm UTC](https://discourse.slicer.org/t/masking-segmentations-disappearing-issue/33500 "2023-12-22T20:15:19Z")

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When I am segmenting, sometimes it will disappear on me. I can see it in the 3D area but not in any of slices. Sometimes, this will happen after I apply thresholding, and other times, it appears to occur randomly. Is the…

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## [Drawing 3D objects](https://discourse.slicer.org/t/drawing-3d-objects/33236)

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**Author:** [@Dejf](https://discourse.slicer.org/u/Dejf)\
**Replies:** 1\
**Last updated:** [December 5, 2023, 4:23pm UTC](https://discourse.slicer.org/t/drawing-3d-objects/33236 "2023-12-05T16:23:30Z")

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Hello, I am trying to segment coronary arteries by thresholding. My idea is to draw two ovoids (or any kind of object with adjustable dimensions in every directions), the first should be bigger that a heart and second sh…

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## [Change default threshold while masking](https://discourse.slicer.org/t/change-default-threshold-while-masking/31416)

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**Author:** [@V11](https://discourse.slicer.org/u/V11)\
**Replies:** 0\
**Last updated:** [August 29, 2023, 6:38am UTC](https://discourse.slicer.org/t/change-default-threshold-while-masking/31416 "2023-08-29T06:38:43Z")

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Operating system: Windows Slicer version: 5.0.3 I have multiple labels to be annotated in a CT volume. I use the Threshold tool followed by “Use for Masking” to paint the region of interest (ROI) . I want to know if t…

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## [issue with exporting seg Dicom files ](https://discourse.slicer.org/t/issue-with-exporting-seg-dicom-files/29556)

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**Author:** [@mustafa\_magdy](https://discourse.slicer.org/u/mustafa_magdy)\
**Replies:** 5\
**Last updated:** [May 21, 2023, 3:33am UTC](https://discourse.slicer.org/t/issue-with-exporting-seg-dicom-files/29556 "2023-05-21T03:33:46Z")

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i downloaded Data from TCIA and its already have a seg results. what i want to do is exporting the segmented lesion out of the whole volume as dicom file to start working on it. what i’m getting after exporting the fil…

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## [An error was reported en route using AI（Lungmask R321） of Lungsegmentation](https://discourse.slicer.org/t/an-error-was-reported-en-route-using-ai-lungmask-r321-of-lungsegmentation/28653)

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**Author:** [@zhenhua3](https://discourse.slicer.org/u/zhenhua3)\
**Replies:** 6\
**Last updated:** [March 29, 2023, 3:32pm UTC](https://discourse.slicer.org/t/an-error-was-reported-en-route-using-ai-lungmask-r321-of-lungsegmentation/28653 "2023-03-29T15:32:28Z")

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Dear development team of LungCTanalyzer or Dear Rudolf Bumm professor I have an error while using your AI program, can you please help me solve this problem？ This is my error record： @rbumm

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## [Volume cropping CT images using lung masks](https://discourse.slicer.org/t/volume-cropping-ct-images-using-lung-masks/28155)

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**Author:** [@Vahdane](https://discourse.slicer.org/u/Vahdane)\
**Replies:** 2\
**Last updated:** [March 3, 2023, 2:58pm UTC](https://discourse.slicer.org/t/volume-cropping-ct-images-using-lung-masks/28155 "2023-03-03T14:58:55Z")

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Hello, I want to crop the lung CT image to lobe subregions by using lung masks. I have the masks, however, as far as I know, we can only crop the image to a rectangular shape in the crop volume module. Thanks for your …

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## [mask volume problem in PET images](https://discourse.slicer.org/t/mask-volume-problem-in-pet-images/27004)

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**Author:** [@bennur](https://discourse.slicer.org/u/bennur)\
**Replies:** 0\
**Last updated:** [January 1, 2023, 6:05pm UTC](https://discourse.slicer.org/t/mask-volume-problem-in-pet-images/27004 "2023-01-01T18:05:59Z")

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Hi everyone, i am using Slicer 4.11 and ı am trying masking tumor volumes on PET images but masked volume can be empty for some PET images . I dont understand why?

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## [Use Mesh to Mask a Segmentation](https://discourse.slicer.org/t/use-mesh-to-mask-a-segmentation/24819)

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**Author:** [@connorh](https://discourse.slicer.org/u/connorh)\
**Replies:** 1\
**Last updated:** [August 18, 2022, 5:36pm UTC](https://discourse.slicer.org/t/use-mesh-to-mask-a-segmentation/24819 "2022-08-18T17:36:43Z")

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Hello, I have a polydata mesh (currently loaded as a modelNode) that I would like to use the geometry to mask a segmentation of the registered CT scan. I’m looking for a way to convert this mesh to a filled segmentation…

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## [Multiply two images using "Multiply Scalar Volumes" or "Mask Scalar Volume" and save the resulting image (using Python)](https://discourse.slicer.org/t/multiply-two-images-using-multiply-scalar-volumes-or-mask-scalar-volume-and-save-the-resulting-image-using-python/10947)

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**Author:** [@Vishal\_P](https://discourse.slicer.org/u/Vishal_P)\
**Replies:** 8\
**Last updated:** [July 26, 2022, 8:14pm UTC](https://discourse.slicer.org/t/multiply-two-images-using-multiply-scalar-volumes-or-mask-scalar-volume-and-save-the-resulting-image-using-python/10947 "2022-07-26T20:14:20Z")

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I am a beginner trying to automate some tasks in 3D Slicer using Python. I have a mask image and another input volume image both in nifti format. how can I use python to automate the multiplication between two images a…

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## [Auto threshold function for a specific area?](https://discourse.slicer.org/t/auto-threshold-function-for-a-specific-area/23080)

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**Author:** [@Jinny\_Lee](https://discourse.slicer.org/u/Jinny_Lee)\
**Replies:** 3\
**Last updated:** [May 2, 2022, 10:27pm UTC](https://discourse.slicer.org/t/auto-threshold-function-for-a-specific-area/23080 "2022-05-02T22:27:31Z")

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Hi, I’m trying to segment a specific area from an FDG PET image and use the “Automatic threshold” function to get an automatic value from the selected area. I’ve tried using the “Masking” function but it didn’t work be…

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## [Mask Shifting in Segment Editor](https://discourse.slicer.org/t/mask-shifting-in-segment-editor/18850)

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**Author:** [@Esteban\_Barreiro](https://discourse.slicer.org/u/Esteban_Barreiro)\
**Replies:** 1\
**Last updated:** [July 21, 2021, 11:56am UTC](https://discourse.slicer.org/t/mask-shifting-in-segment-editor/18850 "2021-07-21T11:56:24Z")

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Hi everybody! hope you are ok. I found that sometimes masks from the Segment Editor shift before zoom in or out in Axial, Sagital and Coronal views. Center the views (even with axial,sagital and coronal views linked) do…

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## [How to save brain structural edited masks (segment edited) in nifti for freesurfer use?](https://discourse.slicer.org/t/how-to-save-brain-structural-edited-masks-segment-edited-in-nifti-for-freesurfer-use/18429)

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**Author:** [@Tamires\_Zanao](https://discourse.slicer.org/u/Tamires_Zanao)\
**Replies:** 1\
**Last updated:** [July 2, 2021, 4:04am UTC](https://discourse.slicer.org/t/how-to-save-brain-structural-edited-masks-segment-edited-in-nifti-for-freesurfer-use/18429 "2021-07-02T04:04:46Z")

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Hi! I automatically generated structural brain masks with the purpose of using FreeSurfer. The masks need some editing, and I used Slicer Segment Editor for it (opened mask as label \> imported labelmap as segmentation \> …

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## [prostatic manual segmentation and mask extraction](https://discourse.slicer.org/t/prostatic-manual-segmentation-and-mask-extraction/17131)

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**Author:** [@Marco\_Catinozzi](https://discourse.slicer.org/u/Marco_Catinozzi)\
**Replies:** 0\
**Last updated:** [April 16, 2021, 1:26pm UTC](https://discourse.slicer.org/t/prostatic-manual-segmentation-and-mask-extraction/17131 "2021-04-16T13:26:20Z")

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Operating system: macOS Big Sur 11.2.3 Slicer version: 4.11.20200930 Hallo folks! Need your help! I am working with a prostatic MRI data set, my boss is suggesting to extract a binary mask and to manually segment the…

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## [threshold masks ](https://discourse.slicer.org/t/threshold-masks/16181)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 0\
**Last updated:** [February 24, 2021, 1:38pm UTC](https://discourse.slicer.org/t/threshold-masks/16181 "2021-02-24T13:38:27Z")

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is it possible to save a mask made by thresholding ? i use different masks for different segments , when i go back i gave to make the threshold mask all over , is there a way around that ? thanks

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## [Using Scissors to make mask on MRI](https://discourse.slicer.org/t/using-scissors-to-make-mask-on-mri/15867)

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**Author:** [@HodaGH](https://discourse.slicer.org/u/HodaGH)\
**Replies:** 3\
**Last updated:** [February 10, 2021, 3:52am UTC](https://discourse.slicer.org/t/using-scissors-to-make-mask-on-mri/15867 "2021-02-10T03:52:09Z")

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Hi all, I’m trying to create a mask for registration of MRI and CT pelvis scans using scissors in segment editor. It works perfectly for CT but when I draw the same free-form area on the MRI the mask only goes half thro…

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## [Volume rendering a masked area](https://discourse.slicer.org/t/volume-rendering-a-masked-area/14637)

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**Author:** [@Jason\_C](https://discourse.slicer.org/u/Jason_C)\
**Replies:** 5\
**Last updated:** [November 17, 2020, 6:48am UTC](https://discourse.slicer.org/t/volume-rendering-a-masked-area/14637 "2020-11-17T06:48:50Z")

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I’d like to use the volume renderer to render a portion of an MRI, but I only want to render the area covered by (a) specific segmentation(s). I’m just learning slicer so this might be a rtfm case, but how can I do this…

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## [Mask scalar volume vs masking within the registration](https://discourse.slicer.org/t/mask-scalar-volume-vs-masking-within-the-registration/7835)

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**Author:** [@labixin](https://discourse.slicer.org/u/labixin)\
**Replies:** 2\
**Last updated:** [August 6, 2019, 2:46am UTC](https://discourse.slicer.org/t/mask-scalar-volume-vs-masking-within-the-registration/7835 "2019-08-06T02:46:06Z")

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Hi everyone, I am now using Slicer 4.11.0 and want to register pre-surgical CT to post-surgical CT (breast). The two images were acquired using different CT table (curved vs flat), and there are some metal markers on th…

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## [Mixing Modules, and Extensions](https://discourse.slicer.org/t/mixing-modules-and-extensions/7596)

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**Author:** [@jazlynn21100](https://discourse.slicer.org/u/jazlynn21100)\
**Replies:** 2\
**Last updated:** [July 16, 2019, 4:55pm UTC](https://discourse.slicer.org/t/mixing-modules-and-extensions/7596 "2019-07-16T16:55:56Z")

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I’ve been digging on the internet for just over a week to try and figure out how to merge modules. From what I have found, it would seem like an extension is my best bet. However, my 3D slicer won’t load the extension ca…

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## [Threshold masking](https://discourse.slicer.org/t/threshold-masking/6833)

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**Author:** [@prorai](https://discourse.slicer.org/u/prorai)\
**Replies:** 3\
**Last updated:** [May 21, 2019, 2:39pm UTC](https://discourse.slicer.org/t/threshold-masking/6833 "2019-05-21T14:39:58Z")

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How can i apply threshold for masking in segmentation process, using python code?