# Beginner Questions

**URL:** https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=12

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

**Page:** 13

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## [Where is ITKConfig.cmake in ITK-5.2.1?](https://discourse.itk.org/t/where-is-itkconfig-cmake-in-itk-5-2-1/5510)

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**Author:** [@Carles\_Lopez](https://discourse.itk.org/u/Carles_Lopez)\
**Replies:** 1\
**Last updated:** [November 21, 2022, 6:14pm UTC](https://discourse.itk.org/t/where-is-itkconfig-cmake-in-itk-5-2-1/5510 "2022-11-21T18:14:08Z")

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Hello to everyone. I’ve installed itk-5.2.1 with pip in an anaconda environment on Python 3.9. On the other hand, I’m trying to run CMake. I’m asked about the directory where ITKConfig.cmake or itk-config. cmake is loc…

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## [How to convert .stl file to mesh data](https://discourse.itk.org/t/how-to-convert-stl-file-to-mesh-data/5488)

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**Author:** [@Zijian\_Hu](https://discourse.itk.org/u/Zijian_Hu)\
**Replies:** 11\
**Last updated:** [November 21, 2022, 2:14pm UTC](https://discourse.itk.org/t/how-to-convert-stl-file-to-mesh-data/5488 "2022-11-21T14:14:19Z")

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Hi, I am trying to convert a .stl file to mesh data. It seems there is no direct way to implement it. So, my idea is first convert the file to a temporary .vtk file and then using itk.meshread() to get the mesh data. Ho…

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## [How do I get a Pointer to an Image](https://discourse.itk.org/t/how-do-i-get-a-pointer-to-an-image/5497)

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**Author:** [@Oddone-Scatena](https://discourse.itk.org/u/Oddone-Scatena)\
**Replies:** 6\
**Last updated:** [November 19, 2022, 2:04am UTC](https://discourse.itk.org/t/how-do-i-get-a-pointer-to-an-image/5497 "2022-11-19T02:04:42Z")

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Hi folks, I am trying to use an Advection Image in the GeodesicActiveCountour segmentation. I think the advection image must be a pointer to an pointer to a vector image. In my case the program asks for a: itk::Image\<i…

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## [Read CT volume compatible to nibabel orientation using SimpleITK](https://discourse.itk.org/t/read-ct-volume-compatible-to-nibabel-orientation-using-simpleitk/5254)

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**Author:** [@isuruwi](https://discourse.itk.org/u/isuruwi)\
**Replies:** 3\
**Last updated:** [November 18, 2022, 12:06pm UTC](https://discourse.itk.org/t/read-ct-volume-compatible-to-nibabel-orientation-using-simpleitk/5254 "2022-11-18T12:06:01Z")

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I want to read the CT volume from simpleITK with compatible to nibabel. When I read the CT volume using nibabel, the orientation (i.e. LAS), image origin, spacing and start, and ending physical points are output as seen…

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## [sitk Commands for N4](https://discourse.itk.org/t/sitk-commands-for-n4/5465)

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**Author:** [@spinicist](https://discourse.itk.org/u/spinicist)\
**Replies:** 7\
**Last updated:** [November 17, 2022, 4:37pm UTC](https://discourse.itk.org/t/sitk-commands-for-n4/5465 "2022-11-17T16:37:19Z")

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Hello, I’d like to add loggin for N4BiasFieldCorrection in sitk, similar to that printed out by the ANTs version. However, it looks like the GetCurrentConvergenceMeasurement and GetCurrentLevel methods are not currentl…

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## [Linking itk with an external project](https://discourse.itk.org/t/linking-itk-with-an-external-project/5481)

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**Author:** [@Ajay\_Emmanuel](https://discourse.itk.org/u/Ajay_Emmanuel)\
**Replies:** 5\
**Last updated:** [November 11, 2022, 7:59pm UTC](https://discourse.itk.org/t/linking-itk-with-an-external-project/5481 "2022-11-11T19:59:16Z")

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Hi, I built the latest version of itk using CMake. After configuring my CMakeLists.txt file in as per the instructions online for an external project, I am still getting this error - cannot open source file “itkImage.h”…

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## [How to change the order of rotation in SetComputeZYX()?](https://discourse.itk.org/t/how-to-change-the-order-of-rotation-in-setcomputezyx/5474)

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**Author:** [@suzume](https://discourse.itk.org/u/suzume)\
**Replies:** 5\
**Last updated:** [November 11, 2022, 1:08am UTC](https://discourse.itk.org/t/how-to-change-the-order-of-rotation-in-setcomputezyx/5474 "2022-11-11T01:08:03Z")

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I want to generate DRR from a CT image. I want the CT image to rotate in the order of the X, Y, Z axis. However, SetComputeZYX( ) only set the order ZYX/ZXY. How can I can set the order XYZ?

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## [What type of transformation aligns the centres of the two volumes?](https://discourse.itk.org/t/what-type-of-transformation-aligns-the-centres-of-the-two-volumes/5470)

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**Author:** [@mahesh\_bhosale](https://discourse.itk.org/u/mahesh_bhosale)\
**Replies:** 4\
**Last updated:** [November 8, 2022, 11:15pm UTC](https://discourse.itk.org/t/what-type-of-transformation-aligns-the-centres-of-the-two-volumes/5470 "2022-11-08T23:15:48Z")

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I am working on the medical image registration task which requires two volumes to be affinely aligned globally, what transformation should I apply to make them aligned?

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## [Processing two images with different starts](https://discourse.itk.org/t/processing-two-images-with-different-starts/5451)

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**Author:** [@Oddone-Scatena](https://discourse.itk.org/u/Oddone-Scatena)\
**Replies:** 1\
**Last updated:** [October 27, 2022, 1:15pm UTC](https://discourse.itk.org/t/processing-two-images-with-different-starts/5451 "2022-10-27T13:15:04Z")

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I have 2 images with the same size but with different starts. I want use one as a mask. Should I use import image filter first to set the same start for both of them?

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## [Adding additional geometries to Viewer changes colours of outputs](https://discourse.itk.org/t/adding-additional-geometries-to-viewer-changes-colours-of-outputs/5449)

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**Author:** [@Kevin\_Sweeney](https://discourse.itk.org/u/Kevin_Sweeney)\
**Replies:** 3\
**Last updated:** [October 26, 2022, 1:30pm UTC](https://discourse.itk.org/t/adding-additional-geometries-to-viewer-changes-colours-of-outputs/5449 "2022-10-26T13:30:18Z")

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I am visualising multiple outputs in the same view depending on choices by the user (i.e. highlighting points on top of glyphs etc). However, I am finding that as I add additional glyphs the colours of other sources cha…

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## [ITK read multi-frame DCM files](https://discourse.itk.org/t/itk-read-multi-frame-dcm-files/5444)

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**Author:** [@itkk](https://discourse.itk.org/u/itkk)\
**Replies:** 3\
**Last updated:** [October 25, 2022, 4:16pm UTC](https://discourse.itk.org/t/itk-read-multi-frame-dcm-files/5444 "2022-10-25T16:16:17Z")

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Can ITK read multi-frame DCM files? For example, DSA, how to do it?

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## [Each voxel (3-dimmensional pixel) in the image has a length, width, and height of 1mm. What will be the volume in cm^3?](https://discourse.itk.org/t/each-voxel-3-dimmensional-pixel-in-the-image-has-a-length-width-and-height-of-1mm-what-will-be-the-volume-in-cm-3/5438)

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**Author:** [@dharmannasdmit](https://discourse.itk.org/u/dharmannasdmit)\
**Replies:** 1\
**Last updated:** [October 23, 2022, 11:51pm UTC](https://discourse.itk.org/t/each-voxel-3-dimmensional-pixel-in-the-image-has-a-length-width-and-height-of-1mm-what-will-be-the-volume-in-cm-3/5438 "2022-10-23T23:51:57Z")

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dimension of image is 256X256X192 T2\_76.IMA (130.1 KB) Each voxel (3-dimmensional pixel) in this image has a length, width, and height of 1mm. Calculate brain volume from brainMask. What is the volume of this brain in …

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## [how to implement registration between DSA(2d)-CTA(3d) image](https://discourse.itk.org/t/how-to-implement-registration-between-dsa-2d-cta-3d-image/5415)

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**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 11\
**Last updated:** [October 21, 2022, 1:56am UTC](https://discourse.itk.org/t/how-to-implement-registration-between-dsa-2d-cta-3d-image/5415 "2022-10-21T01:56:12Z")

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Is there any method to register DSA(2d)-CTA(3d) images? For every point in CTA, I want to know the corresponding point in DSA. I find an example for 2d-3d registration. In this ITKTwoProjectionRegistration, I don’t know…

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## [import image axis reorder and flipping](https://discourse.itk.org/t/import-image-axis-reorder-and-flipping/5433)

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**Author:** [@leandro328](https://discourse.itk.org/u/leandro328)\
**Replies:** 2\
**Last updated:** [October 20, 2022, 8:06pm UTC](https://discourse.itk.org/t/import-image-axis-reorder-and-flipping/5433 "2022-10-20T20:06:21Z")

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i need to work with itk images and numpy arrays, but the operations itk.GetImageFromArray and itk.GetArrayFromImage e.g.: img = itk.GetImageFromArray(input\_img) res\_img = itk.GetArrayFromImage(img) are flipping and a…

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## [Ability to show text actor in itkwidgets.view()](https://discourse.itk.org/t/ability-to-show-text-actor-in-itkwidgets-view/5431)

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**Author:** [@Kevin\_Sweeney](https://discourse.itk.org/u/Kevin_Sweeney)\
**Replies:** 0\
**Last updated:** [October 20, 2022, 3:18pm UTC](https://discourse.itk.org/t/ability-to-show-text-actor-in-itkwidgets-view/5431 "2022-10-20T15:18:49Z")

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I am just looking to confirm that it is not possible to add BillboardTextActor3D to viewer geometries. I have tried a few things, but as the warning stipulates: The 'geometries' trait of a Viewer instance expected A dat…

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## [Retrieve info on current itkwidget.view window bounds - following zoom](https://discourse.itk.org/t/retrieve-info-on-current-itkwidget-view-window-bounds-following-zoom/5420)

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**Author:** [@Kevin\_Sweeney](https://discourse.itk.org/u/Kevin_Sweeney)\
**Replies:** 4\
**Last updated:** [October 19, 2022, 6:19pm UTC](https://discourse.itk.org/t/retrieve-info-on-current-itkwidget-view-window-bounds-following-zoom/5420 "2022-10-19T18:19:31Z")

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As point selection in itkwidgets.view is not currently possible (Geometry / Point selection · Issue #575 · Kitware/itk-vtk-viewer · GitHub) is there a way to get the visual bounds of the viewer? i.e. if we create a view …

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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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## [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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## [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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## [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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## [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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## [\[Solved\] 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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## [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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## [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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## [ITK 5.2.1 static build Win x64](https://discourse.itk.org/t/itk-5-2-1-static-build-win-x64/5341)

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**Author:** [@DL\_I](https://discourse.itk.org/u/DL_I)\
**Replies:** 3\
**Last updated:** [September 20, 2022, 5:56am UTC](https://discourse.itk.org/t/itk-5-2-1-static-build-win-x64/5341 "2022-09-20T05:56:16Z")

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building ITK tag v5.2.1 static in Visual Studio 2020 x64 build environment. I have Qt 5.15.2, VTK 9.1.0 and GDCM 3.1.0 built statically debug. ITK is configured to use\_system\_gdcm, shared libs off, no testing, no e…

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## [How to open .TRE file?](https://discourse.itk.org/t/how-to-open-tre-file/2538)

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**Author:** [@Duy\_H](https://discourse.itk.org/u/Duy_H)\
**Replies:** 64\
**Last updated:** [September 19, 2022, 11:33am UTC](https://discourse.itk.org/t/how-to-open-tre-file/2538 "2022-09-19T11:33:30Z")

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Dataset at “https://public.kitware.com/Wiki/TubeTK/Data” have “VascularNetwork.tre” file. How can i open this file using Python?

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## [DRR Generation from 3D Chest CT and Projection of a Mesh onto the DRR](https://discourse.itk.org/t/drr-generation-from-3d-chest-ct-and-projection-of-a-mesh-onto-the-drr/5325)

<div class="topic-metadata">

**Author:** [@qod\_rec](https://discourse.itk.org/u/qod_rec)\
**Replies:** 7\
**Last updated:** [September 16, 2022, 5:31pm UTC](https://discourse.itk.org/t/drr-generation-from-3d-chest-ct-and-projection-of-a-mesh-onto-the-drr/5325 "2022-09-16T17:31:07Z")

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Hello everyone. I have 3D chest CTs whose lung contour is labeled and I generate the contour meshes. I am trying to complete the following things: Generate the DRR from the 3D chest CTs Project the mesh vertex(points…

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