# Latest

**URL:** https://discourse.itk.org/latest.md?page=32

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

**Page:** 33

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## [Registration: at image border + noisy images](https://discourse.itk.org/t/registration-at-image-border-noisy-images/5419)

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**Author:** [@dyoll](https://discourse.itk.org/u/dyoll)\
**Replies:** 5\
**Last updated:** [October 18, 2022, 7:40pm UTC](https://discourse.itk.org/t/registration-at-image-border-noisy-images/5419 "2022-10-18T19:40:09Z")

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I am trying to register a vertebrae atlas to a dataset of T1 images. Using a jupyter notebook GUI we have created relatively good initial transforms to align the template masks to the dataset. I was hoping to be able to…

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## [Trait Error: The 'children' trait of a VBox instance ...](https://discourse.itk.org/t/trait-error-the-children-trait-of-a-vbox-instance/5416)

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**Author:** [@Kevin\_Sweeney](https://discourse.itk.org/u/Kevin_Sweeney)\
**Replies:** 3\
**Last updated:** [October 17, 2022, 7:56am UTC](https://discourse.itk.org/t/trait-error-the-children-trait-of-a-vbox-instance/5416 "2022-10-17T07:56:34Z")

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I am getting the error: TraitError: The 'children' trait of a VBox instance contains an Instance of a TypedTuple which expected a Widget, not the Viewer at '0x2aaab5d0ad00'. when running the code below in Jupyter Lab i…

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## [Why should a Composite Filter disconnect its input?](https://discourse.itk.org/t/why-should-a-composite-filter-disconnect-its-input/5410)

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**Author:** [@SteveRobbins](https://discourse.itk.org/u/SteveRobbins)\
**Replies:** 3\
**Last updated:** [October 14, 2022, 8:55pm UTC](https://discourse.itk.org/t/why-should-a-composite-filter-disconnect-its-input/5410 "2022-10-14T20:55:04Z")

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Hello, Working in C++ ITK 5.2.1, I have been writing a few filter classes, following the guidance of Chapter 8 (“How To Write A Composite Filter”) of the ITK guide book. I think I have a reasonable grasp of the materia…

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## [How to remove the CT scanning bed with SimpleITK](https://discourse.itk.org/t/how-to-remove-the-ct-scanning-bed-with-simpleitk/5392)

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**Author:** [@kleingeo](https://discourse.itk.org/u/kleingeo)\
**Replies:** 8\
**Last updated:** [October 14, 2022, 12:25am UTC](https://discourse.itk.org/t/how-to-remove-the-ct-scanning-bed-with-simpleitk/5392 "2022-10-14T00:25:23Z")

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I currently have CT scans that have the scanner bed in the image. I was wondering if someone knew of a method to crop out the bed from the images with SimpleITK. I have seen some work using 3D Slicer, but as this is part…

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## [ThinPlateSplineWarp using landmarks](https://discourse.itk.org/t/thinplatesplinewarp-using-landmarks/5413)

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**Author:** [@Nicolas\_Loiseau](https://discourse.itk.org/u/Nicolas_Loiseau)\
**Replies:** 0\
**Last updated:** [October 13, 2022, 3:42pm UTC](https://discourse.itk.org/t/thinplatesplinewarp-using-landmarks/5413 "2022-10-13T15:42:46Z")

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Hello everything, I am new to this forum, so please forgive me if my post is not consistent. I’m using itk c++. My goal is to register two volumes with non rigid transformation (nifti volumes, from a medical dataset), …

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## [OTSU thresholding binary image](https://discourse.itk.org/t/otsu-thresholding-binary-image/5409)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 1\
**Last updated:** [October 12, 2022, 12:59pm UTC](https://discourse.itk.org/t/otsu-thresholding-binary-image/5409 "2022-10-12T12:59:34Z")

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Hi, does any one have any sample data for OTSU thresholding that i could use. I refer to the example Threshold An Image Using OTSU? Here is the link: https://examples.itk.org/src/filtering/thresholding/thresholdanimage…

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## [3D ellipse hough transform](https://discourse.itk.org/t/3d-ellipse-hough-transform/2861)

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**Author:** [@basal](https://discourse.itk.org/u/basal)\
**Replies:** 1\
**Last updated:** [October 12, 2022, 10:36am UTC](https://discourse.itk.org/t/3d-ellipse-hough-transform/2861 "2022-10-12T10:36:06Z")

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Hi all, I want to extend 2D hough transform to 3D and also use ellipse function instead of circles in ITK based on c++ to detect ellipse shapes in my image. I changed some lines of the 2D Hough transform code for ellipse…

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## [Adding support for customizing ITK namespace](https://discourse.itk.org/t/adding-support-for-customizing-itk-namespace/5170)

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**Author:** [@jcfr](https://discourse.itk.org/u/jcfr)\
**Replies:** 13\
**Last updated:** [October 11, 2022, 2:09pm UTC](https://discourse.itk.org/t/adding-support-for-customizing-itk-namespace/5170 "2022-10-11T14:09:29Z")

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Plan We propose to update ITK to support customizing the ITK namespace. Motivation These change will allow importing itk python modules into application themselves built against ITK and ensure filter execution return va…

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## [Modify an element in a matrix](https://discourse.itk.org/t/modify-an-element-in-a-matrix/5398)

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**Author:** [@zhuangming.shen](https://discourse.itk.org/u/zhuangming.shen)\
**Replies:** 7\
**Last updated:** [October 11, 2022, 9:53am UTC](https://discourse.itk.org/t/modify-an-element-in-a-matrix/5398 "2022-10-11T09:53:56Z")

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Hi, if I want to modify an element in a matrix, in ITK 4.13.3, I can code like But in ITK 5.2.1, the same code seems fail to change the element. I’d like to know what’s the way to do this in ITK 5. Thanks in advan…

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## [itkwidgets large images](https://discourse.itk.org/t/itkwidgets-large-images/5401)

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**Author:** [@darrent1974](https://discourse.itk.org/u/darrent1974)\
**Replies:** 2\
**Last updated:** [October 10, 2022, 7:02pm UTC](https://discourse.itk.org/t/itkwidgets-large-images/5401 "2022-10-10T19:02:37Z")

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Hi, I’m currently using itkwidgets 1.0a6 and was wondering if there is any internal limit on displaying 2D images above a certain size? In my current testing I’ve discovered that the view widget stops rendering images …

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## [I had trouble using SiddonJacobsRayCastInterpolateImageFunction](https://discourse.itk.org/t/i-had-trouble-using-siddonjacobsraycastinterpolateimagefunction/5310)

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**Author:** [@hcs027](https://discourse.itk.org/u/hcs027)\
**Replies:** 1\
**Last updated:** [October 7, 2022, 6:39pm UTC](https://discourse.itk.org/t/i-had-trouble-using-siddonjacobsraycastinterpolateimagefunction/5310 "2022-10-07T18:39:34Z")

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I had trouble using SiddonJacobsRayCastInterpolateImageFunction. I could install itk and itk-twoprojectionregistration. I can find the SiddonJacobsRayCastInterpolateImageFunction module during dir (itk). But when I try t…

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## [How to compute Target Registration Error (TRE) of Rigid Body Registration in SITK?](https://discourse.itk.org/t/how-to-compute-target-registration-error-tre-of-rigid-body-registration-in-sitk/5292)

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**Author:** [@debapriya](https://discourse.itk.org/u/debapriya)\
**Replies:** 7\
**Last updated:** [October 7, 2022, 1:12pm UTC](https://discourse.itk.org/t/how-to-compute-target-registration-error-tre-of-rigid-body-registration-in-sitk/5292 "2022-10-07T13:12:02Z")

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Hello, I am trying to find out TRE of 3D Multimodal Rigid Medical Image Registration using metric JointHistogramMutualInformation. The TRE function of SimpleITK takes a list of landmark points from the fixed and moving …

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## [Reduced dependencies for ITK external modules](https://discourse.itk.org/t/reduced-dependencies-for-itk-external-modules/5391)

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**Author:** [@dyoll](https://discourse.itk.org/u/dyoll)\
**Replies:** 7\
**Last updated:** [October 7, 2022, 12:54pm UTC](https://discourse.itk.org/t/reduced-dependencies-for-itk-external-modules/5391 "2022-10-07T12:54:06Z")

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I would like to reduce dependencies to only the minimal ITK modules, instead of pulling in all of itk from pypi. Since my code only depends on ITKCommon I tried using itk-core as dependency. I did pip install itk\_dis…

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## [How to set points in gui?](https://discourse.itk.org/t/how-to-set-points-in-gui/5386)

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**Author:** [@debapriya](https://discourse.itk.org/u/debapriya)\
**Replies:** 4\
**Last updated:** [October 7, 2022, 8:58am UTC](https://discourse.itk.org/t/how-to-set-points-in-gui/5386 "2022-10-07T08:58:16Z")

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I have a set of 3D coordinate points. fixed\_image\_points = \[ (156.48434676356158, 201.92274575468412, 68.0), (194.25413436597393, 98.55771047484492, 32.0), (128.94523819661913, 96.18284152323203, 32.0), \] mo…

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## [Zero-valued spacing is not supported and may result in undefined behavior.](https://discourse.itk.org/t/zero-valued-spacing-is-not-supported-and-may-result-in-undefined-behavior/5382)

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**Author:** [@orena1](https://discourse.itk.org/u/orena1)\
**Replies:** 6\
**Last updated:** [October 7, 2022, 1:22am UTC](https://discourse.itk.org/t/zero-valued-spacing-is-not-supported-and-may-result-in-undefined-behavior/5382 "2022-10-07T01:22:35Z")

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Hi, I am trying to run a python registration package and I get an error This is the code that I run: irm.SetMetricAsMattesMutualInformation(numberOfHistogramBins=256) irm.SetMetricFixedMask(fix\_mask) irm.SetMetricMov…

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## [\`Apply Morphological Closing on Specific Label Object\` Example, Label value? radius value?](https://discourse.itk.org/t/apply-morphological-closing-on-specific-label-object-example-label-value-radius-value/5387)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 1\
**Last updated:** [October 6, 2022, 6:49pm UTC](https://discourse.itk.org/t/apply-morphological-closing-on-specific-label-object-example-label-value-radius-value/5387 "2022-10-06T18:49:00Z")

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Hi, what values for label and radius should be used? I am working on Labeling objects for segmentation of 2D/3D and i came accros Labeling concept. I know usually Label would be in range of 0-255 so i figured it is abo…

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## [Convert image dtypes](https://discourse.itk.org/t/convert-image-dtypes/5389)

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**Author:** [@JonB](https://discourse.itk.org/u/JonB)\
**Replies:** 1\
**Last updated:** [October 6, 2022, 12:45pm UTC](https://discourse.itk.org/t/convert-image-dtypes/5389 "2022-10-06T12:45:14Z")

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Hi there, I have a problem regarding storage of transformed images. I applied several filters on 3D images and now I see after transformation the dtype changed because of the transformation from int16 (original image) …

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## [difference between resample result in c++ version and python version](https://discourse.itk.org/t/difference-between-resample-result-in-c-version-and-python-version/5374)

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**Author:** [@SummerZ2020](https://discourse.itk.org/u/SummerZ2020)\
**Replies:** 2\
**Last updated:** [September 30, 2022, 2:49am UTC](https://discourse.itk.org/t/difference-between-resample-result-in-c-version-and-python-version/5374 "2022-09-30T02:49:05Z")

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Hello all, I am using ITK to resample CT 3D volume. I have done two version, one is c++, one is python. The difference between their result is not small. The bigger difference is existed in boundary part in the image.BT…

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## [ChangeInformationImageFilter missing from Pip-installed ITK 5.3rc4post3](https://discourse.itk.org/t/changeinformationimagefilter-missing-from-pip-installed-itk-5-3rc4post3/5375)

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**Author:** [@mchinand](https://discourse.itk.org/u/mchinand)\
**Replies:** 2\
**Last updated:** [September 29, 2022, 7:21pm UTC](https://discourse.itk.org/t/changeinformationimagefilter-missing-from-pip-installed-itk-5-3rc4post3/5375 "2022-09-29T19:21:44Z")

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When I try to use ChangeInformationImageFilter I get attributeError: module 'itk' has no attribute 'ChangeInformationImageFilter' after upgrading to ITK5.3rc4. I’m trying to use it with code that worked with 5.2.1. I ra…

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## [Segmentation to text file](https://discourse.itk.org/t/segmentation-to-text-file/5377)

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**Author:** [@Sean\_Hatton](https://discourse.itk.org/u/Sean_Hatton)\
**Replies:** 1\
**Last updated:** [September 29, 2022, 7:02pm UTC](https://discourse.itk.org/t/segmentation-to-text-file/5377 "2022-09-29T19:02:42Z")

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Hi all, I would like to export my segmentations to a text file (i.e. list of contour pixels) to create IMOD model files (with point2model). Two questions: I expect I would push the segmentation through the LabelContou…

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## [\[Solved\] BSplineTransformation from displacement vectors](https://discourse.itk.org/t/solved-bsplinetransformation-from-displacement-vectors/5372)

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**Author:** [@Flemingjp](https://discourse.itk.org/u/Flemingjp)\
**Replies:** 5\
**Last updated:** [September 29, 2022, 10:50am UTC](https://discourse.itk.org/t/solved-bsplinetransformation-from-displacement-vectors/5372 "2022-09-29T10:50:47Z")

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I have pairs of points that describes the displacement between one image to another image. How can I use these points to construct a BSplineTransform? An example of these points \[0 0\] -\> \[18.53 57.52 \] \[76 0\] -\> \[90.7…

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## [How I can use my projection image stack to reconstruct them using RTK](https://discourse.itk.org/t/how-i-can-use-my-projection-image-stack-to-reconstruct-them-using-rtk/3281)

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**Author:** [@shaleenanuj](https://discourse.itk.org/u/shaleenanuj)\
**Replies:** 3\
**Last updated:** [September 28, 2022, 8:45am UTC](https://discourse.itk.org/t/how-i-can-use-my-projection-image-stack-to-reconstruct-them-using-rtk/3281 "2022-09-28T08:45:22Z")

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Hello sir, I have projection images taken with a cone-beam source, how using RTK can I reconstruct them. I am new to RTK-ITK. Is there any sample program where I can plug in my data. I am using Python as a platform. I…

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## [Difference between RANDOM, REGULAR and NONE sampling](https://discourse.itk.org/t/difference-between-random-regular-and-none-sampling/5365)

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**Author:** [@debapriya](https://discourse.itk.org/u/debapriya)\
**Replies:** 3\
**Last updated:** [September 27, 2022, 6:57pm UTC](https://discourse.itk.org/t/difference-between-random-regular-and-none-sampling/5365 "2022-09-27T18:57:06Z")

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I have run the same registration code snippet, with the same data and same sampling strategy, multiple times. I get different result each time. With RANDOM sampling, this is understandable, but why should REGULAR and NON…

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## [Update image within itkwidgets.view](https://discourse.itk.org/t/update-image-within-itkwidgets-view/5366)

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**Author:** [@Kevin\_Sweeney](https://discourse.itk.org/u/Kevin_Sweeney)\
**Replies:** 7\
**Last updated:** [September 27, 2022, 2:22pm UTC](https://discourse.itk.org/t/update-image-within-itkwidgets-view/5366 "2022-09-27T14:22:36Z")

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I am using itkwidgets.view to show a .vtk object in Jupyter. If I run the following, it shows as expected: image = itk.imread('exampleImageData/mri.vtk') self.activeView = itkwidgets.view(image=image, rotate=True, back…

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## [itk::imageSeriesReader return nullptr](https://discourse.itk.org/t/itk-imageseriesreader-return-nullptr/5367)

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**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 2\
**Last updated:** [September 27, 2022, 1:55pm UTC](https://discourse.itk.org/t/itk-imageseriesreader-return-nullptr/5367 "2022-09-27T13:55:54Z")

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using InputImageTypeCuda = itk::CudaImage\<float, 3\>; using ReaderTypeCuda = itk::ImageSeriesReader; ReaderTypeCuda::Pointer reader = ReaderTypeCuda::New(); ReaderTypeCuda::New() failed it return nullptr, anyone know w…

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## [Advice on on-line processing of time series](https://discourse.itk.org/t/advice-on-on-line-processing-of-time-series/5330)

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**Author:** [@SteveRobbins](https://discourse.itk.org/u/SteveRobbins)\
**Replies:** 8\
**Last updated:** [September 26, 2022, 7:36pm UTC](https://discourse.itk.org/t/advice-on-on-line-processing-of-time-series/5330 "2022-09-26T19:36:21Z")

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I’m writing code that accepts a time series of 3D images and want to process it on-line; i.e. as they come in. I’m not seeing this topic discussed so maybe it’s too esoteric or maybe I haven’t found the right keywords. …

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## [How to calculate eigen values and eigen vectors of an image](https://discourse.itk.org/t/how-to-calculate-eigen-values-and-eigen-vectors-of-an-image/5361)

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**Author:** [@cnkhanh](https://discourse.itk.org/u/cnkhanh)\
**Replies:** 2\
**Last updated:** [September 26, 2022, 1:33pm UTC](https://discourse.itk.org/t/how-to-calculate-eigen-values-and-eigen-vectors-of-an-image/5361 "2022-09-26T13:33:56Z")

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I tried to calculate eigen values and eigen vectors of an image by getting the array of the image img = sitk.ReadImage("data/image.mhd") img\_arr = sitk.GetArrayFromImage(img) w, v = numpy.linalg.eig(img\_arr) But I go…

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## [How to combine images](https://discourse.itk.org/t/how-to-combine-images/5359)

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**Author:** [@cnkhanh](https://discourse.itk.org/u/cnkhanh)\
**Replies:** 1\
**Last updated:** [September 26, 2022, 1:08pm UTC](https://discourse.itk.org/t/how-to-combine-images/5359 "2022-09-26T13:08:14Z")

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I have four images (1 channel): CT, airtree, vessels, lobes. I tried to combine as below, ref\_img = sitk.ReadImage("data/ct.hdr", sitk.sitkInt8) vessel\_img = sitk.ReadImage("data/vessels.hdr", sitk.sitkInt8) airway\_img …

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## [Point selection within itkwidgets](https://discourse.itk.org/t/point-selection-within-itkwidgets/5356)

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**Author:** [@Kevin\_Sweeney](https://discourse.itk.org/u/Kevin_Sweeney)\
**Replies:** 1\
**Last updated:** [September 22, 2022, 4:50pm UTC](https://discourse.itk.org/t/point-selection-within-itkwidgets/5356 "2022-09-22T16:50:05Z")

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I am generating a 2/3 dimensional array of glyphs which are being visualised within Jupyter Notebooks using itkwidgets Something along the line of self.glyphs = vtk.vtkGlyph3D() ... projectionView = itkwidgets.view(g…

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## [Does sery share the same rescale slope?](https://discourse.itk.org/t/does-sery-share-the-same-rescale-slope/5348)

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**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 4\
**Last updated:** [September 22, 2022, 1:38pm UTC](https://discourse.itk.org/t/does-sery-share-the-same-rescale-slope/5348 "2022-09-22T13:38:41Z")

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I want to read dicom files, and I want to know whether the sery share the same rescale slope/intercept? Or two image in one sery may have different rescale slope/intercept.

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