# Beginner Questions

**URL:** https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=4

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

**Page:** 5

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## [Marker registration does not follow image registration](https://discourse.itk.org/t/marker-registration-does-not-follow-image-registration/6691)

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**Author:** [@sebquet](https://discourse.itk.org/u/sebquet)\
**Replies:** 4\
**Last updated:** [June 11, 2024, 8:57pm UTC](https://discourse.itk.org/t/marker-registration-does-not-follow-image-registration/6691 "2024-06-11T20:57:02Z")

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Hello, I registered an MRI scan to a CT scan as follows: tx = sitk.AffineTransform(fixed\_image.GetDimension()) init\_pos = sitk.CenteredTransformInitializerFilter.MOMENTS initial\_transform = sitk.CenteredTransformIniti…

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## [FDK Reconstruction error](https://discourse.itk.org/t/fdk-reconstruction-error/6680)

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**Author:** [@akshara](https://discourse.itk.org/u/akshara)\
**Replies:** 2\
**Last updated:** [June 11, 2024, 5:59am UTC](https://discourse.itk.org/t/fdk-reconstruction-error/6680 "2024-06-11T05:59:57Z")

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We’re currently engaged in CBCT reconstruction and have successfully developed a Python-based code for the task, which functions without issue. However, encountering an error during the conversion process to C++, specifi…

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## [Compiling Issue with ITKVtkGlue](https://discourse.itk.org/t/compiling-issue-with-itkvtkglue/6304)

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**Author:** [@MartinHeller](https://discourse.itk.org/u/MartinHeller)\
**Replies:** 2\
**Last updated:** [June 8, 2024, 10:48pm UTC](https://discourse.itk.org/t/compiling-issue-with-itkvtkglue/6304 "2024-06-08T22:48:29Z")

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Hi everyone I like to compile Plastimatch with ITK/VTK. During the configuration, I got following error: Plastimatch version is 1.9.4-49-g581c7692 CMake Error at //lib/cmake/ITK-5.3/Modules/ITKVtkGlue.cmake:16 (find\_p…

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## [How to plot the figure shown in the website](https://discourse.itk.org/t/how-to-plot-the-figure-shown-in-the-website/6674)

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**Author:** [@Kyle-RuidongLI](https://discourse.itk.org/u/Kyle-RuidongLI)\
**Replies:** 5\
**Last updated:** [June 6, 2024, 1:44pm UTC](https://discourse.itk.org/t/how-to-plot-the-figure-shown-in-the-website/6674 "2024-06-06T13:44:05Z")

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Hello, everyone! I am new to SimpleITK. I was attracted by the excellent figure shown in the website for illustrating “An abundance of filters for image segmentation workflows, from classics such as Otsu thresholding to …

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## [Is it possible to create a user-defined cost function for registration?](https://discourse.itk.org/t/is-it-possible-to-create-a-user-defined-cost-function-for-registration/6677)

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**Author:** [@Vidya](https://discourse.itk.org/u/Vidya)\
**Replies:** 0\
**Last updated:** [June 6, 2024, 7:35am UTC](https://discourse.itk.org/t/is-it-possible-to-create-a-user-defined-cost-function-for-registration/6677 "2024-06-06T07:35:45Z")

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Hi, I am trying register two images with Bspline. I tried with itk::MeanSquaresImageToImageMetricv4 and itk::MattesMutualInformationImageToImageMetricv4. Both doesn’t give the correct registration for all the images. I w…

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## [SimpleITK Euler3D transform, problem with output size/resampling](https://discourse.itk.org/t/simpleitk-euler3d-transform-problem-with-output-size-resampling/4387)

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**Author:** [@MMdeB](https://discourse.itk.org/u/MMdeB)\
**Replies:** 7\
**Last updated:** [May 29, 2024, 1:45am UTC](https://discourse.itk.org/t/simpleitk-euler3d-transform-problem-with-output-size-resampling/4387 "2024-05-29T01:45:10Z")

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Hi there, I’m trying to rotate a 3D volume using the Euler3D transform. For this, I first used the code below, but I found that the image size does not change if the image is rotated, which is explainable since I use in…

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## [Floating point issue in mhd header file](https://discourse.itk.org/t/floating-point-issue-in-mhd-header-file/6643)

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**Author:** [@fool2nd](https://discourse.itk.org/u/fool2nd)\
**Replies:** 8\
**Last updated:** [May 25, 2024, 6:25pm UTC](https://discourse.itk.org/t/floating-point-issue-in-mhd-header-file/6643 "2024-05-25T18:25:27Z")

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Hi, I ran into a problem when writing an image to mhd/raw file. Here’s the code snippet. import SimpleITK as sitk image = sitk.ReadImage(‘image.mhd’) print(image.GetSpacing()) (0.002, 0.002, 0.002) image.SetSpacin…

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## [Convert Itk Mesh to VtK Polydata](https://discourse.itk.org/t/convert-itk-mesh-to-vtk-polydata/6564)

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**Author:** [@NahomKidane](https://discourse.itk.org/u/NahomKidane)\
**Replies:** 5\
**Last updated:** [May 21, 2024, 12:34pm UTC](https://discourse.itk.org/t/convert-itk-mesh-to-vtk-polydata/6564 "2024-05-21T12:34:11Z")

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Hello, Is there a way to convert ITKMesh to vtkpolydata? I see ITKMeshToPolyData, but that converts ITKMesh to ITKPolydata.

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## [Registration of two sequence images of 2d each](https://discourse.itk.org/t/registration-of-two-sequence-images-of-2d-each/6641)

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**Author:** [@sivanschwartz](https://discourse.itk.org/u/sivanschwartz)\
**Replies:** 1\
**Last updated:** [May 20, 2024, 1:12pm UTC](https://discourse.itk.org/t/registration-of-two-sequence-images-of-2d-each/6641 "2024-05-20T13:12:32Z")

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Hi all, I am new to SimpleITK, and will appreciate any tips for how to start to deal with my issue: I have a data of 2 images from brain scan, with slightly different depth (one image is from Zi depth of the brain, and…

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## [Is itk.js support "StreamingImageFilter"?](https://discourse.itk.org/t/is-itk-js-support-streamingimagefilter/6605)

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**Author:** [@Mohammed\_AboArab](https://discourse.itk.org/u/Mohammed_AboArab)\
**Replies:** 2\
**Last updated:** [May 20, 2024, 10:52am UTC](https://discourse.itk.org/t/is-itk-js-support-streamingimagefilter/6605 "2024-05-20T10:52:35Z")

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Hello, I am currently working on 3D volume rendering using vtk.js and itk.js. I encountered an issue when rendering a large-sized dataset, which is related to MemoryAllocationError. After some investigation, I discovere…

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## [Read different series of dicom](https://discourse.itk.org/t/read-different-series-of-dicom/6251)

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**Author:** [@Xoz](https://discourse.itk.org/u/Xoz)\
**Replies:** 8\
**Last updated:** [May 20, 2024, 4:13am UTC](https://discourse.itk.org/t/read-different-series-of-dicom/6251 "2024-05-20T04:13:43Z")

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Hi everyone, I’ve got an issue when loading some dicom files using itk-wasm, in the past I load the uploaded files through readImageDICOMFileSeries, it worked fine when there is just a single serie. But some of the dic…

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## [How to filter dicom images using a kernel?](https://discourse.itk.org/t/how-to-filter-dicom-images-using-a-kernel/6610)

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**Author:** [@dbtruong](https://discourse.itk.org/u/dbtruong)\
**Replies:** 1\
**Last updated:** [May 19, 2024, 9:11pm UTC](https://discourse.itk.org/t/how-to-filter-dicom-images-using-a-kernel/6610 "2024-05-19T21:11:33Z")

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Hello everyone, I use itk.js for some web image processing functionality. How to filter dicom images using itk.js? Thanks.

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## [Getting Started/installation](https://discourse.itk.org/t/getting-started-installation/6596)

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**Author:** [@Arnaud](https://discourse.itk.org/u/Arnaud)\
**Replies:** 5\
**Last updated:** [May 19, 2024, 3:13pm UTC](https://discourse.itk.org/t/getting-started-installation/6596 "2024-05-19T15:13:43Z")

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Hi all, I have a “could not find any instance of Visual Studio” error upon clicking “Configure” in CMake. I have zero knowledge about ITK/RTK yet apart from the ITKSoftwareGuide book1 that i started reading. I do alre…

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## [How to get intermediate transform parameter?](https://discourse.itk.org/t/how-to-get-intermediate-transform-parameter/6631)

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**Author:** [@Vidya](https://discourse.itk.org/u/Vidya)\
**Replies:** 2\
**Last updated:** [May 14, 2024, 5:57am UTC](https://discourse.itk.org/t/how-to-get-intermediate-transform-parameter/6631 "2024-05-14T05:57:31Z")

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Hi, I am following the example DeformableRegistration12 : ITK: Examples/RegistrationITKv4/DeformableRegistration12.cxx , to register two images. Is there any way to get the intermediate transform parameters or intermedi…

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## [ImageSeriesReader for dicom series and PixelIDValue of sitkFloat64](https://discourse.itk.org/t/imageseriesreader-for-dicom-series-and-pixelidvalue-of-sitkfloat64/6630)

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**Author:** [@Ervis](https://discourse.itk.org/u/Ervis)\
**Replies:** 4\
**Last updated:** [May 13, 2024, 1:38pm UTC](https://discourse.itk.org/t/imageseriesreader-for-dicom-series-and-pixelidvalue-of-sitkfloat64/6630 "2024-05-13T13:38:01Z")

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I have a strange question ( it may very well be from my lack of understanding) so thank you in advance I am using SimpleITK-2.3.0-CSharp-win64-x64 to read and manipulate MR images . I have an MR series with the followi…

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## [Stacking Z dimension images using SimpleITK](https://discourse.itk.org/t/stacking-z-dimension-images-using-simpleitk/6623)

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**Author:** [@sleepingcat4](https://discourse.itk.org/u/sleepingcat4)\
**Replies:** 26\
**Last updated:** [May 13, 2024, 1:04pm UTC](https://discourse.itk.org/t/stacking-z-dimension-images-using-simpleitk/6623 "2024-05-13T13:04:59Z")

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I’m trying to stack multiple Z dimension images where the images are taken in XYZ axis. (Images are in .tiff format) I want those 2D images to create a 3D Volume. I was tinkering with SimpleITK on Python, I got some res…

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## [Binary segmentation dilation in mm](https://discourse.itk.org/t/binary-segmentation-dilation-in-mm/6628)

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**Author:** [@tanres](https://discourse.itk.org/u/tanres)\
**Replies:** 1\
**Last updated:** [May 10, 2024, 9:41pm UTC](https://discourse.itk.org/t/binary-segmentation-dilation-in-mm/6628 "2024-05-10T21:41:44Z")

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I am looking to perform dilation of a binary segmentation by a certain mm radius. E.g., dilate the segmentation of the lung by 5-10mm, so I can use it as a registration mask to focus image registration. Is the kernel rad…

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## [How to retrieve meta-data of HDF5 Dataset?](https://discourse.itk.org/t/how-to-retrieve-meta-data-of-hdf5-dataset/6619)

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**Author:** [@debapriya](https://discourse.itk.org/u/debapriya)\
**Replies:** 1\
**Last updated:** [May 7, 2024, 7:41pm UTC](https://discourse.itk.org/t/how-to-retrieve-meta-data-of-hdf5-dataset/6619 "2024-05-07T19:41:10Z")

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Hello, I have a 3D brain image (MR) in .mat format. I have used the following code to access the image data. import SimpleITK as sitk import numpy as np import h5py f = h5py.File('MR.mat','r') data\_value = f\['Data1\_an…

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## [CT and PET coregistration with alternating results](https://discourse.itk.org/t/ct-and-pet-coregistration-with-alternating-results/5691)

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**Author:** [@Keyn34](https://discourse.itk.org/u/Keyn34)\
**Replies:** 4\
**Last updated:** [May 1, 2024, 1:26pm UTC](https://discourse.itk.org/t/ct-and-pet-coregistration-with-alternating-results/5691 "2024-05-01T13:26:14Z")

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Hello everyone, I am a bit confused about the registration results I got from performing a rigid alignment between a CT and a PET (of the same subject, which makes it even more confusing for me). I can run it once and g…

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## [ApproximateSignedDistanceMapImageFilter does not support any pixel type](https://discourse.itk.org/t/approximatesigneddistancemapimagefilter-does-not-support-any-pixel-type/6594)

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**Author:** [@M-Puig](https://discourse.itk.org/u/M-Puig)\
**Replies:** 1\
**Last updated:** [April 25, 2024, 12:51pm UTC](https://discourse.itk.org/t/approximatesigneddistancemapimagefilter-does-not-support-any-pixel-type/6594 "2024-04-25T12:51:20Z")

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Hi, I am trying to compute a distance map on a binary 3d shape, using ApproximateSignedDistanceMapImageFilter. I tried the following code def get\_radius\_map(mask): dist\_filter = sitk.ApproximateSignedDistanceMapIm…

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## [Visualize Images at each Pyramid Level](https://discourse.itk.org/t/visualize-images-at-each-pyramid-level/6497)

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**Author:** [@kenrickmoke](https://discourse.itk.org/u/kenrickmoke)\
**Replies:** 1\
**Last updated:** [April 24, 2024, 7:54pm UTC](https://discourse.itk.org/t/visualize-images-at-each-pyramid-level/6497 "2024-04-24T19:54:59Z")

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Heya Itk-Team, how can i visualize the downsampled\\smooted images at each level of the pyramid for image registration, here i am mostly interested in the fixed image. Im using itk-elastix for python. Best wishes …

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## [SimpleITK-SimpleElastix- can't install different release versions](https://discourse.itk.org/t/simpleitk-simpleelastix-cant-install-different-release-versions/6272)

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**Author:** [@edelarosa](https://discourse.itk.org/u/edelarosa)\
**Replies:** 5\
**Last updated:** [April 22, 2024, 6:50am UTC](https://discourse.itk.org/t/simpleitk-simpleelastix-cant-install-different-release-versions/6272 "2024-04-22T06:50:37Z")

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Hello, I am trying to download SimpleITK-SImpleElastix 2.0.0rc2.dev910 from SimpleITK-SimpleElastix · PyPI using pip, but the following error appears: ERROR: Could not find a version that satisfies the requirement Sim…

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## [ITK Affine transform doesn't translate the image as expected](https://discourse.itk.org/t/itk-affine-transform-doesnt-translate-the-image-as-expected/6584)

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**Author:** [@Erezke](https://discourse.itk.org/u/Erezke)\
**Replies:** 0\
**Last updated:** [April 18, 2024, 5:45am UTC](https://discourse.itk.org/t/itk-affine-transform-doesnt-translate-the-image-as-expected/6584 "2024-04-18T05:45:40Z")

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Hi I am trying to translate a DICOM image using an affine transform to a new position, but when I compare the centers of both images (before/after) it seems like the image did not move. Following is the code I use: ...…

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## [\[Question\] Python not found during compilation](https://discourse.itk.org/t/question-python-not-found-during-compilation/6580)

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**Author:** [@Suzaku](https://discourse.itk.org/u/Suzaku)\
**Replies:** 1\
**Last updated:** [April 17, 2024, 1:03pm UTC](https://discourse.itk.org/t/question-python-not-found-during-compilation/6580 "2024-04-17T13:03:15Z")

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Hi, I’m trying to compile SimpleITK with SimpleElastix in a ubuntu 20.04.6 LTS system. I’ve used the following command as suggested in the documentation: git clone GitHub - SimpleITK/SimpleITK: SimpleITK: a layer built o…

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## [Fill small holes in the segmentation label image](https://discourse.itk.org/t/fill-small-holes-in-the-segmentation-label-image/6575)

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**Author:** [@G\_Y](https://discourse.itk.org/u/G_Y)\
**Replies:** 6\
**Last updated:** [April 16, 2024, 2:16pm UTC](https://discourse.itk.org/t/fill-small-holes-in-the-segmentation-label-image/6575 "2024-04-16T14:16:01Z")

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Hi all, I have done a Sitk.MorphologicalWatershed to my image and got a label image, I find there are some small segments of one or two pixels, or like this little “cross”: What would be the best filter/way to fill th…

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## [Landmark Image Registration of Images with different Resolutions](https://discourse.itk.org/t/landmark-image-registration-of-images-with-different-resolutions/6573)

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**Author:** [@luviku](https://discourse.itk.org/u/luviku)\
**Replies:** 2\
**Last updated:** [April 16, 2024, 7:16am UTC](https://discourse.itk.org/t/landmark-image-registration-of-images-with-different-resolutions/6573 "2024-04-16T07:16:24Z")

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Hello everyone, I am a beginner so please forgive me if this is a basic question. I am working on registering Spectralis SLO images with OCT-A images. I am using landmarks to identify points on vessels, which correlate …

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## [Failed to import SimpleITK in Python following its installation through miniconda on Win11-x64](https://discourse.itk.org/t/failed-to-import-simpleitk-in-python-following-its-installation-through-miniconda-on-win11-x64/6460)

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**Author:** [@ms-hashemi](https://discourse.itk.org/u/ms-hashemi)\
**Replies:** 4\
**Last updated:** [April 15, 2024, 3:35pm UTC](https://discourse.itk.org/t/failed-to-import-simpleitk-in-python-following-its-installation-through-miniconda-on-win11-x64/6460 "2024-04-15T15:35:28Z")

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Hi everyone, I would like to work with SimpleITK in Python. It seems that it has been installed successfully via miniconda on my Win11-x64 system, but when I try to import it in the interactive environment of Python, I …

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## [Sitk C# Scale Image Up](https://discourse.itk.org/t/sitk-c-scale-image-up/6561)

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**Author:** [@G\_Y](https://discourse.itk.org/u/G_Y)\
**Replies:** 4\
**Last updated:** [April 12, 2024, 2:22pm UTC](https://discourse.itk.org/t/sitk-c-scale-image-up/6561 "2024-04-12T14:22:30Z")

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Hi all, I want to scale up an image twice as big using Sitk C#: var img = Sitk.ReadImage(file); var scale = new ScaleTransform(2, new VectorDouble(2) { 0.5, 0.5 }); var imageScaled = Sitk.Resample(img, scale, Interpolat…

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## [ITK Image Direction vs DICOM Image Orientation (Patient)](https://discourse.itk.org/t/itk-image-direction-vs-dicom-image-orientation-patient/6364)

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**Author:** [@aditya](https://discourse.itk.org/u/aditya)\
**Replies:** 3\
**Last updated:** [April 9, 2024, 7:47am UTC](https://discourse.itk.org/t/itk-image-direction-vs-dicom-image-orientation-patient/6364 "2024-04-09T07:47:25Z")

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I am working with a directory containing sagittal DICOM images. Here is how I obtain Image Orientation (DICOM tag 0020,0037) using pydicom. from pydicom import dcmread import os dcm\_dir = r"path/to/dicom/dir/sagittal\_a…

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## [Support ROI projection to isocenter?](https://discourse.itk.org/t/support-roi-projection-to-isocenter/6555)

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**Author:** [@zhangyx007](https://discourse.itk.org/u/zhangyx007)\
**Replies:** 1\
**Last updated:** [April 7, 2024, 6:24pm UTC](https://discourse.itk.org/t/support-roi-projection-to-isocenter/6555 "2024-04-07T18:24:05Z")

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ITK support ROI projection to isocenter? if support, which example can help me？ thanks。

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