# \#threshold

**URL:** https://discourse.slicer.org/tag/threshold/20.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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## [How to use local threshold](https://discourse.slicer.org/t/how-to-use-local-threshold/40909)

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**Author:** [@Dan\_Cheng](https://discourse.slicer.org/u/Dan_Cheng)\
**Replies:** 3\
**Last updated:** [January 3, 2025, 10:49pm UTC](https://discourse.slicer.org/t/how-to-use-local-threshold/40909 "2025-01-03T22:49:23Z")

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Hi I am trying to using local threshold in 5.6.2. When I press cmd + left click, there is no segment at all. Can anyone help me? Many thanks!

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## [Reconstructing a 3D volume from 2D slices](https://discourse.slicer.org/t/reconstructing-a-3d-volume-from-2d-slices/37846)

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**Author:** [@Trung\_L\_i\_Quang](https://discourse.slicer.org/u/Trung_L_i_Quang)\
**Replies:** 11\
**Last updated:** [August 15, 2024, 3:49pm UTC](https://discourse.slicer.org/t/reconstructing-a-3d-volume-from-2d-slices/37846 "2024-08-15T15:49:11Z")

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Dear community, I am a newbie to 3D Slicer and I’m hoping to get some advice! I have a dataset consisting of 1700 2D image slices (60GB total) originally in 16-bit TIFF format. I converted these to 8-bit JPEGs (400MB t…

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## [Segment thresholding with multiple transforms](https://discourse.slicer.org/t/segment-thresholding-with-multiple-transforms/35982)

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**Author:** [@bruce](https://discourse.slicer.org/u/bruce)\
**Replies:** 2\
**Last updated:** [May 8, 2024, 8:21pm UTC](https://discourse.slicer.org/t/segment-thresholding-with-multiple-transforms/35982 "2024-05-08T20:21:45Z")

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Hello This might be a bit obscure but I note inconsistent behaviour with the Segment Editor Threshold tool when working with a segmentation based on a volume with nested transforms. In particular, the thresholding range…

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## [Export segment threshold](https://discourse.slicer.org/t/export-segment-threshold/34083)

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**Author:** [@juedcrt](https://discourse.slicer.org/u/juedcrt)\
**Replies:** 0\
**Last updated:** [February 1, 2024, 12:03pm UTC](https://discourse.slicer.org/t/export-segment-threshold/34083 "2024-02-01T12:03:45Z")

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Operating system: Windows Slicer version: 5.4.0 Expected behavior: Actual behavior: Hello I am trying to manually segment brain lesions. I find that the threshold tool helps me to delineate these lesions but once I…

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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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## [Lateral Ventricles of the Brain](https://discourse.slicer.org/t/lateral-ventricles-of-the-brain/29763)

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**Author:** [@elliotw4](https://discourse.slicer.org/u/elliotw4)\
**Replies:** 0\
**Last updated:** [June 1, 2023, 12:08am UTC](https://discourse.slicer.org/t/lateral-ventricles-of-the-brain/29763 "2023-06-01T00:08:56Z")

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I’m currently trying to export STL models of the lateral ventricles of the brain of various sizes: enlarged, average, and slit. Almost all of my smaller or slit ventricle models have some kind of tissue (I believe choroi…

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## [Information about the local thresholding effect's algorithms](https://discourse.slicer.org/t/information-about-the-local-thresholding-effects-algorithms/29456)

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**Author:** [@paolo](https://discourse.slicer.org/u/paolo)\
**Replies:** 2\
**Last updated:** [May 14, 2023, 8:05pm UTC](https://discourse.slicer.org/t/information-about-the-local-thresholding-effects-algorithms/29456 "2023-05-14T20:05:46Z")

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Hi everyone! I’m using the local threshold effect to segment different kinds of tissues (eg. lung parenchyma), and I was wondering about how does the segmentation algorithms work in the extension. I read that the effec…

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## [Threshold in the segment editor](https://discourse.slicer.org/t/threshold-in-the-segment-editor/29316)

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**Author:** [@duan](https://discourse.slicer.org/u/duan)\
**Replies:** 1\
**Last updated:** [May 6, 2023, 2:40pm UTC](https://discourse.slicer.org/t/threshold-in-the-segment-editor/29316 "2023-05-06T14:40:14Z")

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What is the threshold in the segment editor? Does this threshold represent the window width of the corresponding CT value of human tissue?

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## [Threshold segmentation of intracranial hemorrhage foci](https://discourse.slicer.org/t/threshold-segmentation-of-intracranial-hemorrhage-foci/29017)

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**Author:** [@duan](https://discourse.slicer.org/u/duan)\
**Replies:** 1\
**Last updated:** [April 20, 2023, 3:41am UTC](https://discourse.slicer.org/t/threshold-segmentation-of-intracranial-hemorrhage-foci/29017 "2023-04-20T03:41:06Z")

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Excuse me,May I confirm that the threshold for segmenting intracranial hemorrhage lesions using threshold segmentation in the segment editor is 40-100?

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## [Local Threshold --\> restrict threshold operation to user-defined 3D region --\> how to?](https://discourse.slicer.org/t/local-threshold-restrict-threshold-operation-to-user-defined-3d-region-how-to/27413)

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**Author:** [@MrMarkus](https://discourse.slicer.org/u/MrMarkus)\
**Replies:** 1\
**Last updated:** [January 23, 2023, 9:26am UTC](https://discourse.slicer.org/t/local-threshold-restrict-threshold-operation-to-user-defined-3d-region-how-to/27413 "2023-01-23T09:26:23Z")

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Operating system: Win10 Slicer version: 5.2.1 r31317 / 77da381 Hi, maybe you could help me out here: I am using “Local Threshold” and the region which should be segmented is further defined by the option “ROI” → Vol…

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## [How to use Python to achieve the thresholding effect of the ‘Volumes’ module? (synchronized with the volume rendering)](https://discourse.slicer.org/t/how-to-use-python-to-achieve-the-thresholding-effect-of-the-volumes-module-synchronized-with-the-volume-rendering/20891)

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**Author:** [@CharlesChen](https://discourse.slicer.org/u/CharlesChen)\
**Replies:** 42\
**Last updated:** [August 2, 2022, 9:35pm UTC](https://discourse.slicer.org/t/how-to-use-python-to-achieve-the-thresholding-effect-of-the-volumes-module-synchronized-with-the-volume-rendering/20891 "2022-08-02T21:35:34Z")

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Hi there, I’m new to 3D Slicer. Currently, I am trying to develop a python scripted module in 3D Slicer. One of the features is to control the threshold of the volume rendering image through a slider. In other words,…

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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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## [Question about applying automatic maximum entropy on the FDG PET image](https://discourse.slicer.org/t/question-about-applying-automatic-maximum-entropy-on-the-fdg-pet-image/23048)

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**Author:** [@Jinny\_Lee](https://discourse.slicer.org/u/Jinny_Lee)\
**Replies:** 3\
**Last updated:** [April 21, 2022, 10:32am UTC](https://discourse.slicer.org/t/question-about-applying-automatic-maximum-entropy-on-the-fdg-pet-image/23048 "2022-04-21T10:32:14Z")

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Hi, I’m currently working on FDG PET images to segment a tumor using automatic maximum entropy. I thought the maximum entropy would be able to automatically segment the tumor, but it selects other organs like the heart …

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## [Changing threshold in python does not update in any views](https://discourse.slicer.org/t/changing-threshold-in-python-does-not-update-in-any-views/20919)

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**Author:** [@koeglfryderyk](https://discourse.slicer.org/u/koeglfryderyk)\
**Replies:** 1\
**Last updated:** [December 6, 2021, 12:06am UTC](https://discourse.slicer.org/t/changing-threshold-in-python-does-not-update-in-any-views/20919 "2021-12-06T00:06:36Z")

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I want to use a shortcut to change the lower threshold of a foreground US volume to 1 (so that the black surrounding pixels disappear). I used the code from here, and this code changes the threshold in the GUI, however,…

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## [Threshold range in Segment Editor includes values outside of range](https://discourse.slicer.org/t/threshold-range-in-segment-editor-includes-values-outside-of-range/20869)

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**Author:** [@koeglfryderyk](https://discourse.slicer.org/u/koeglfryderyk)\
**Replies:** 0\
**Last updated:** [December 1, 2021, 6:41pm UTC](https://discourse.slicer.org/t/threshold-range-in-segment-editor-includes-values-outside-of-range/20869 "2021-12-01T18:41:04Z")

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I’m using Slicer 4.11.20210226 on Windows 11. I want to create a segmentation of all values greater than zero. When I set the lower threshold to e.g. 0.2 it still includes pixels with values equal to zero (you can see …

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## [Threshold in Segment Editor does not apply Segmentation](https://discourse.slicer.org/t/threshold-in-segment-editor-does-not-apply-segmentation/13937)

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**Author:** [@Fadyed](https://discourse.slicer.org/u/Fadyed)\
**Replies:** 2\
**Last updated:** [October 8, 2020, 4:57pm UTC](https://discourse.slicer.org/t/threshold-in-segment-editor-does-not-apply-segmentation/13937 "2020-10-08T16:57:47Z")

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Operating system:Win Slicer version:4.10.2 Expected behavior: Apply threshold segmentation after successful preview Actual behavior: “Apply” does nothing. segmentation is erased if Module or Tool are switched I ne…

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## [Threshold picking up too many voxels. How do I segment different areas with same voxels without having to manually paint it? ](https://discourse.slicer.org/t/threshold-picking-up-too-many-voxels-how-do-i-segment-different-areas-with-same-voxels-without-having-to-manually-paint-it/11476)

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**Author:** [@Demi\_Trimino](https://discourse.slicer.org/u/Demi_Trimino)\
**Replies:** 1\
**Last updated:** [May 10, 2020, 11:35am UTC](https://discourse.slicer.org/t/threshold-picking-up-too-many-voxels-how-do-i-segment-different-areas-with-same-voxels-without-having-to-manually-paint-it/11476 "2020-05-10T11:35:42Z")

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Operating system: Mac Slicer version: 4-11-0 Expected behavior: Actual behavior: I want to just segment the outline (cuticle) but the inner muscles are too similar in intensity and threshold keeps picking them up. H…

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## [Spine segmentation in cervico-thoracic region](https://discourse.slicer.org/t/spine-segmentation-in-cervico-thoracic-region/11234)

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**Author:** [@Ricardoneuro](https://discourse.slicer.org/u/Ricardoneuro)\
**Replies:** 4\
**Last updated:** [April 28, 2020, 9:01pm UTC](https://discourse.slicer.org/t/spine-segmentation-in-cervico-thoracic-region/11234 "2020-04-28T21:01:24Z")

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Hi community, It´s being very difficult to segment a spine in a dual quality aquisition dataset. This happens, for example, in the the cervical-thoracic transition of the spine. If someone else is in this issue please …

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## [Cannot paint segments outside a certain region in an MRI image](https://discourse.slicer.org/t/cannot-paint-segments-outside-a-certain-region-in-an-mri-image/9710)

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**Author:** [@momosukh](https://discourse.slicer.org/u/momosukh)\
**Replies:** 1\
**Last updated:** [January 5, 2020, 4:07am UTC](https://discourse.slicer.org/t/cannot-paint-segments-outside-a-certain-region-in-an-mri-image/9710 "2020-01-05T04:07:19Z")

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I am facing a weird issue, I am unable to paint the layer of the outer abdomen, fat, using paint, draw, and other techniques, as shown as the red circle in the figure. The ROI of the area is well spaced in all 3 coordina…

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## [Trouble segmenting the Tongue, after fixing threshold](https://discourse.slicer.org/t/trouble-segmenting-the-tongue-after-fixing-threshold/7907)

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**Author:** [@Raid](https://discourse.slicer.org/u/Raid)\
**Replies:** 3\
**Last updated:** [August 14, 2019, 3:58am UTC](https://discourse.slicer.org/t/trouble-segmenting-the-tongue-after-fixing-threshold/7907 "2019-08-14T03:58:42Z")

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Operating system: Windows 10 Enterprise Slicer version: 4.10.2 Data type: NRRD Hello, I’m working on a human fetal head stained with Phosphotungstic acid (PTA) to be able to visualize soft tissue. I’ve used the sciss…

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## [Cannot apply Threshold on ROI](https://discourse.slicer.org/t/cannot-apply-threshold-on-roi/7269)

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**Author:** [@Apex](https://discourse.slicer.org/u/Apex)\
**Replies:** 3\
**Last updated:** [June 21, 2019, 10:22am UTC](https://discourse.slicer.org/t/cannot-apply-threshold-on-roi/7269 "2019-06-21T10:22:29Z")

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Operating system: Windows, Linux, and Mac Slicer version:4.10.2 Expected behavior: Issue 1: To “apply” “Threshold” on ROI Issue 2: Can apply “Threshold”, but it is automatically reduced to a smaller region when I pres…

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## [Threshold/Hounsfield unit For different series](https://discourse.slicer.org/t/threshold-hounsfield-unit-for-different-series/5930)

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**Author:** [@prorai](https://discourse.slicer.org/u/prorai)\
**Replies:** 1\
**Last updated:** [February 26, 2019, 1:47pm UTC](https://discourse.slicer.org/t/threshold-hounsfield-unit-for-different-series/5930 "2019-02-26T13:47:22Z")

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Hi i’m using the Slicer from few days , and i saw that for different series the threshold value is different for same body part. for example bone threshold value for each body part should be same but it doesn’t work simi…

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## [Threshold segmentation apply issue](https://discourse.slicer.org/t/threshold-segmentation-apply-issue/4731)

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**Author:** [@EricWilson](https://discourse.slicer.org/u/EricWilson)\
**Replies:** 3\
**Last updated:** [November 12, 2018, 6:23pm UTC](https://discourse.slicer.org/t/threshold-segmentation-apply-issue/4731 "2018-11-12T18:23:41Z")

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I am currently having an issue with thresholding an imported ultrasound scan. when i am setting the thresholding values, the area to be affected is shown as i would expect, like this: however, after the threshold oper…

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## [Masking in General Registration](https://discourse.slicer.org/t/masking-in-general-registration/488)

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**Author:** [@Ivan\_Hidrovo](https://discourse.slicer.org/u/Ivan_Hidrovo)\
**Replies:** 1\
**Last updated:** [June 13, 2017, 11:45am UTC](https://discourse.slicer.org/t/masking-in-general-registration/488 "2017-06-13T11:45:52Z")

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Hello community, Does anybody know how to input my own created 0-1 bit mask for general registration (BRAINS) in 3D slicer? Thank you, Ivan

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## [Threshold on Segment](https://discourse.slicer.org/t/threshold-on-segment/258)

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**Author:** [@basti](https://discourse.slicer.org/u/basti)\
**Replies:** 4\
**Last updated:** [May 7, 2017, 10:01pm UTC](https://discourse.slicer.org/t/threshold-on-segment/258 "2017-05-07T22:01:57Z")

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I'm trying to threshold a volume to a created segment. Unfortunately the segment will be empty. What did I forget? # create SegmentationNode and Segment # self.segmentationNode = slicer.vtkMRMLSegmentationNode…