# \#segmentation

**URL:** https://discourse.itk.org/tag/segmentation/195.md

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

---

## [Registation of two vascular images using Python Simple ITK](https://discourse.itk.org/t/registation-of-two-vascular-images-using-python-simple-itk/7766)

<div class="topic-metadata">

**Author:** [@anatolejimenez](https://discourse.itk.org/u/anatolejimenez)\
**Replies:** 1\
**Last updated:** [May 22, 2026, 12:51pm UTC](https://discourse.itk.org/t/registation-of-two-vascular-images-using-python-simple-itk/7766 "2026-05-22T12:51:09Z")

</div>

Hi, I would like to register two vascular images of the same modality but with different dynamics. I played a lot with the image registration metrics (correlation, mutual information and correlation) with optimizer grad…

---

## [Copy headers / metadata between segmentations of different resolutions](https://discourse.itk.org/t/copy-headers-metadata-between-segmentations-of-different-resolutions/6558)

<div class="topic-metadata">

**Author:** [@Cristobal\_Rodero](https://discourse.itk.org/u/Cristobal_Rodero)\
**Replies:** 1\
**Last updated:** [April 9, 2024, 7:28pm UTC](https://discourse.itk.org/t/copy-headers-metadata-between-segmentations-of-different-resolutions/6558 "2024-04-09T19:28:37Z")

</div>

I have a coarse segmentation that I smooth, and the smoothing techniques overwrites the header. I want to retrieve the original one but I have had no success so far. The headers are \_, coarse\_header = nrrd.re…

---

## [Image metrics that incorporate segmentation into registration](https://discourse.itk.org/t/image-metrics-that-incorporate-segmentation-into-registration/6223)

<div class="topic-metadata">

**Author:** [@beastwood](https://discourse.itk.org/u/beastwood)\
**Replies:** 1\
**Last updated:** [September 27, 2023, 8:18pm UTC](https://discourse.itk.org/t/image-metrics-that-incorporate-segmentation-into-registration/6223 "2023-09-27T20:18:33Z")

</div>

I am looking for a way to incorporate the results of image segmentation into an image registration framework and would love some feedback or advice on several possible avenues to pursue. Similar to @dyoll’s question (Me…

---

## [How to use ITK to segment bones in osteoporotic patients](https://discourse.itk.org/t/how-to-use-itk-to-segment-bones-in-osteoporotic-patients/6181)

<div class="topic-metadata">

**Author:** [@AeBoPi](https://discourse.itk.org/u/AeBoPi)\
**Replies:** 2\
**Last updated:** [September 6, 2023, 4:12pm UTC](https://discourse.itk.org/t/how-to-use-itk-to-segment-bones-in-osteoporotic-patients/6181 "2023-09-06T16:12:28Z")

</div>

Osteoporosis reduces bone density and thus the strength of bone in the CT data set (shown in the figure), making it impossible to use traditional thresholding techniques to handle segmentation. I noticed that the M…

---

## [How to automatically refine segmentation warped by deformation field (from voxelmorph).](https://discourse.itk.org/t/how-to-automatically-refine-segmentation-warped-by-deformation-field-from-voxelmorph/5901)

<div class="topic-metadata">

**Author:** [@BraveDistribution](https://discourse.itk.org/u/BraveDistribution)\
**Replies:** 12\
**Last updated:** [June 15, 2023, 5:22am UTC](https://discourse.itk.org/t/how-to-automatically-refine-segmentation-warped-by-deformation-field-from-voxelmorph/5901 "2023-06-15T05:22:56Z")

</div>

Hello, I work on cardiac cycle analysis (TEE). We want to obtain a mask of the left ventricle (or any other region of interest) during the whole cycle based on the mask manually annotated in ED/ES (end of diastole/systo…

---

## [Remove Noisy Objects](https://discourse.itk.org/t/remove-noisy-objects/5492)

<div class="topic-metadata">

**Author:** [@cristinamontserrat](https://discourse.itk.org/u/cristinamontserrat)\
**Replies:** 1\
**Last updated:** [November 16, 2022, 3:12pm UTC](https://discourse.itk.org/t/remove-noisy-objects/5492 "2022-11-16T15:12:28Z")

</div>

Hi! I am trying to remove labels from Label Map, which belong to noisy objects. For doing that, I have created the following code: ITKImgLabelType2D::Pointer RemoveNoisyObjects( const ITKImgLabelType2D::Pointer& imgIn,…

---

## [Blob Detection](https://discourse.itk.org/t/blob-detection/5299)

<div class="topic-metadata">

**Author:** [@Mahdiye\_Imanpanah](https://discourse.itk.org/u/Mahdiye_Imanpanah)\
**Replies:** 1\
**Last updated:** [August 29, 2022, 12:46pm UTC](https://discourse.itk.org/t/blob-detection/5299 "2022-08-29T12:46:45Z")

</div>

Hi everybody I want to develop a method to detect shapes in the images(for example blobs). I’ve found Hough-Transform to reach this goal, but I can’t find it in SimpleItk. Does SimpleItk support Hough-Transform? If i…

---

## [Remove multiple labels in 1 bone and have only 1 label per bone](https://discourse.itk.org/t/remove-multiple-labels-in-1-bone-and-have-only-1-label-per-bone/5186)

<div class="topic-metadata">

**Author:** [@Vilma\_Bozgo](https://discourse.itk.org/u/Vilma_Bozgo)\
**Replies:** 5\
**Last updated:** [July 15, 2022, 2:14pm UTC](https://discourse.itk.org/t/remove-multiple-labels-in-1-bone-and-have-only-1-label-per-bone/5186 "2022-07-15T14:14:29Z")

</div>

Hello! I have a multilabel skeleton mask for MRI images of the skeleton. But for the same bone I sometimes get different labels, like in the image attached where the first bone gets a red label and a green label. But in …

---

## [Semiautomatic Segmentation with SimpleITK](https://discourse.itk.org/t/semiautomatic-segmentation-with-simpleitk/5040)

<div class="topic-metadata">

**Author:** [@shqipcop](https://discourse.itk.org/u/shqipcop)\
**Replies:** 4\
**Last updated:** [June 6, 2022, 8:37am UTC](https://discourse.itk.org/t/semiautomatic-segmentation-with-simpleitk/5040 "2022-06-06T08:37:53Z")

</div>

I’m interested in using SimpleITK to be able to seed an organ in a layer of a CT scan and have the organ segmented, ignoring small connections like veins/arteries. eg. I select a part of the right atrium, the whole right…

---

## [3D SLIC Visualisation](https://discourse.itk.org/t/3d-slic-visualisation/5010)

<div class="topic-metadata">

**Author:** [@aliabidi](https://discourse.itk.org/u/aliabidi)\
**Replies:** 1\
**Last updated:** [May 25, 2022, 11:42pm UTC](https://discourse.itk.org/t/3d-slic-visualisation/5010 "2022-05-25T23:42:40Z")

</div>

As a follow-up from this question regarding SLIC segmentation in 2D, I was wondering whether there is any method or technique to visualise images in 3D? Something similar to the image below from this paper. To give s…

---

## [3d segmentation refinement](https://discourse.itk.org/t/3d-segmentation-refinement/4993)

<div class="topic-metadata">

**Author:** [@AmericaBG](https://discourse.itk.org/u/AmericaBG)\
**Replies:** 4\
**Last updated:** [May 19, 2022, 5:34pm UTC](https://discourse.itk.org/t/3d-segmentation-refinement/4993 "2022-05-19T17:34:29Z")

</div>

Hi! I’ve a 3d mask segmentation that I would like to improve by using some method. For example, something like use the mask like a “seed” and refine the segmentation with the original image information. Original image …

---

## [Inverting Resample Filter Execute operation](https://discourse.itk.org/t/inverting-resample-filter-execute-operation/4856)

<div class="topic-metadata">

**Author:** [@BraveDistribution](https://discourse.itk.org/u/BraveDistribution)\
**Replies:** 16\
**Last updated:** [March 16, 2022, 7:28pm UTC](https://discourse.itk.org/t/inverting-resample-filter-execute-operation/4856 "2022-03-16T19:28:10Z")

</div>

Hello, The problem that I am trying to solve with SimpleITK: 1/ I have a temporal sequence of volumes from the same patient 2/ I have one segmentation mask of the organ under observation. 3/ I want to get segmentatio…

---

## [How to convert multi region Segmentation.seg.nrrd into a set of binary label images?](https://discourse.itk.org/t/how-to-convert-multi-region-segmentation-seg-nrrd-into-a-set-of-binary-label-images/4391)

<div class="topic-metadata">

**Author:** [@machadoL](https://discourse.itk.org/u/machadoL)\
**Replies:** 12\
**Last updated:** [December 10, 2021, 9:29am UTC](https://discourse.itk.org/t/how-to-convert-multi-region-segmentation-seg-nrrd-into-a-set-of-binary-label-images/4391 "2021-12-10T09:29:50Z")

</div>

Hello, friends. I would like to ask your help for converting a 2D segmentation.seg.nrrd into a collection of 2D binary label images (one image per segmentation region). I need to perform that by command line in python …

---

## [Edit a segmentation programatically in simpleitk](https://discourse.itk.org/t/edit-a-segmentation-programatically-in-simpleitk/4512)

<div class="topic-metadata">

**Author:** [@kliron](https://discourse.itk.org/u/kliron)\
**Replies:** 6\
**Last updated:** [October 20, 2021, 7:07pm UTC](https://discourse.itk.org/t/edit-a-segmentation-programatically-in-simpleitk/4512 "2021-10-20T19:07:57Z")

</div>

Hello, I’m very new to itk/simpleitk. What I need to do is: Segment a volume in an image A (I do this in 3D Slicer, manually). In simpleitk, apply the segmentation in another image, B (assume A and B are different…