# Beginner Questions

**URL:** https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=23

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

**Page:** 24

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## [Saving ITKWidgets settings](https://discourse.itk.org/t/saving-itkwidgets-settings/3821)

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**Author:** [@dchen](https://discourse.itk.org/u/dchen)\
**Replies:** 3\
**Last updated:** [February 1, 2021, 8:58pm UTC](https://discourse.itk.org/t/saving-itkwidgets-settings/3821 "2021-02-01T20:58:34Z")

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How can I save and restore the transfer function in ITKWidgets? After I’ve fiddled with the transfer function widgets, I’d like to be able to save the rendering state so that I can restore and share the visualization.

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## [Embarcadero RAD C ++ Studio 10.2.3 Tokyo Architec + ITK + VTK?](https://discourse.itk.org/t/embarcadero-rad-c-studio-10-2-3-tokyo-architec-itk-vtk/1142)

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**Author:** [@Armando](https://discourse.itk.org/u/Armando)\
**Replies:** 3\
**Last updated:** [January 31, 2021, 11:25pm UTC](https://discourse.itk.org/t/embarcadero-rad-c-studio-10-2-3-tokyo-architec-itk-vtk/1142 "2021-01-31T23:25:16Z")

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Is it possible to use Embarcadero RAD C ++ Studio 10.2.3 Tokyo Architec to build applications using ITK e and VTK? Is there a place where you explain how to do it? For ITK and VTK they always refer to compile it and use …

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## [Can not get dicom tag](https://discourse.itk.org/t/can-not-get-dicom-tag/3814)

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**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 1\
**Last updated:** [January 31, 2021, 7:22pm UTC](https://discourse.itk.org/t/can-not-get-dicom-tag/3814 "2021-01-31T19:22:11Z")

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I want to read a dicom tag, and the code is: import SimpleITK as sitk reader = sitk.ImageFileReader() reader.SetFileName(path) reader.LoadPrivateTagsOn() reader.ReadImageInformation() val = reader.GetMetaData('0040|9225…

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## [How to read points and radius info of .vtk file into ITK program](https://discourse.itk.org/t/how-to-read-points-and-radius-info-of-vtk-file-into-itk-program/3339)

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**Author:** [@Henco](https://discourse.itk.org/u/Henco)\
**Replies:** 8\
**Last updated:** [January 29, 2021, 7:37pm UTC](https://discourse.itk.org/t/how-to-read-points-and-radius-info-of-vtk-file-into-itk-program/3339 "2021-01-29T19:37:47Z")

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Hi all, My goal is to register 2d/3d vessel networks. The first step I’ve done is to use the VMTK module in slicer to segment out and calculate the radii of each centerline point. This saves as a .vtk file. However, whi…

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## [Image type for an ITK image from numpy array](https://discourse.itk.org/t/image-type-for-an-itk-image-from-numpy-array/2348)

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**Author:** [@hina-shah](https://discourse.itk.org/u/hina-shah)\
**Replies:** 5\
**Last updated:** [January 29, 2021, 7:32pm UTC](https://discourse.itk.org/t/image-type-for-an-itk-image-from-numpy-array/2348 "2021-01-29T19:32:41Z")

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Here’s a piece of code I’m trying to run using pydicom and itk (using pydicom for a better dicom tag extraction since itk was failing to get some tags). ds = pydicom.read\_file(file\_path) np\_image = ds.pixel\_array itk…

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## [Missing methods](https://discourse.itk.org/t/missing-methods/3795)

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**Author:** [@Brumeux](https://discourse.itk.org/u/Brumeux)\
**Replies:** 6\
**Last updated:** [January 28, 2021, 9:51pm UTC](https://discourse.itk.org/t/missing-methods/3795 "2021-01-28T21:51:55Z")

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Hello, I am trying to use sitk with Unity (C#). I have added the native and managed dll to my project. I tried to follow the fundamental concepts here https://simpleitk.readthedocs.io/en/master/fundamentalConcepts.html …

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## [Extract brain from 3D binary mask images](https://discourse.itk.org/t/extract-brain-from-3d-binary-mask-images/3791)

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**Author:** [@lisongang-PR](https://discourse.itk.org/u/lisongang-PR)\
**Replies:** 2\
**Last updated:** [January 26, 2021, 12:22pm UTC](https://discourse.itk.org/t/extract-brain-from-3d-binary-mask-images/3791 "2021-01-26T12:22:13Z")

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I got the 3D mask of brain by using StripTsImageFilter，How can I use mask to extract brain？

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## [SimpleITK doesn't seem to apply rescale intercept/slop](https://discourse.itk.org/t/simpleitk-doesnt-seem-to-apply-rescale-intercept-slop/3768)

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**Author:** [@malteekj](https://discourse.itk.org/u/malteekj)\
**Replies:** 8\
**Last updated:** [January 22, 2021, 2:32pm UTC](https://discourse.itk.org/t/simpleitk-doesnt-seem-to-apply-rescale-intercept-slop/3768 "2021-01-22T14:32:14Z")

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I’m using the SimpleITK API for python to load medical images in DICOM format (PET and CT). However, it appears that SimpleITK doesn’t apply the rescale slope and rescale intercept. My code right now is: import SimpleIT…

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## [Errors of ITK.js Hello World project](https://discourse.itk.org/t/errors-of-itk-js-hello-world-project/3784)

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**Author:** [@K.Matsuzaki](https://discourse.itk.org/u/K.Matsuzaki)\
**Replies:** 3\
**Last updated:** [January 22, 2021, 4:12am UTC](https://discourse.itk.org/t/errors-of-itk-js-hello-world-project/3784 "2021-01-22T04:12:37Z")

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Hi, I’m interested in ITK.js and trying a Hello World project.(https://insightsoftwareconsortium.github.io/itk-js/examples/hello\_world\_node.html) I installed tools as instructions. Then I executed “npx itk-js build .”…

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## [ITK Snap Registration - Background turns white with rotation or translation](https://discourse.itk.org/t/itk-snap-registration-background-turns-white-with-rotation-or-translation/3788)

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**Author:** [@ckronman](https://discourse.itk.org/u/ckronman)\
**Replies:** 1\
**Last updated:** [January 21, 2021, 8:40pm UTC](https://discourse.itk.org/t/itk-snap-registration-background-turns-white-with-rotation-or-translation/3788 "2021-01-21T20:40:12Z")

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Hello there! I’m using ITK Snap to reorient the translation & rotation of a set of MRI images with the manual registration tool. Everything has been working well until recently when I had an image background change from …

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## [MRI isotropic volume reconstruction from 2D slices](https://discourse.itk.org/t/mri-isotropic-volume-reconstruction-from-2d-slices/3764)

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**Author:** [@Fleur](https://discourse.itk.org/u/Fleur)\
**Replies:** 10\
**Last updated:** [January 18, 2021, 10:24pm UTC](https://discourse.itk.org/t/mri-isotropic-volume-reconstruction-from-2d-slices/3764 "2021-01-18T22:24:26Z")

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Hello everyone, I have a simple task to achieve: I have 3 sets of anisotropic MRI data per subject (= 2D MRI slices along one axis) and I want to perform volume reconstruction to obtain a single 3D isotropic volume of t…

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## [Find default values of parameters for optimizer](https://discourse.itk.org/t/find-default-values-of-parameters-for-optimizer/3738)

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**Author:** [@user1](https://discourse.itk.org/u/user1)\
**Replies:** 3\
**Last updated:** [December 31, 2020, 1:31am UTC](https://discourse.itk.org/t/find-default-values-of-parameters-for-optimizer/3738 "2020-12-31T01:31:15Z")

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Hi! I’m using SimpleITK with Python and am doing a registration task. I used the Powell optimizer and it’s default values worked very well for me so now I’d like to know what they are. I have yet to find a way to access…

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## [Nifti read failed?](https://discourse.itk.org/t/nifti-read-failed/3735)

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**Author:** [@jeffppp](https://discourse.itk.org/u/jeffppp)\
**Replies:** 2\
**Last updated:** [December 30, 2020, 3:36am UTC](https://discourse.itk.org/t/nifti-read-failed/3735 "2020-12-30T03:36:45Z")

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Hello, every one~ I have a question. std::string str=“D:\\Test2.nii”; itk::ImageIOBase::Pointer imageIO = tk::ImageIOFactory::CreateImageIO(str.c\_str(), itk::CommonEnums::IOFileMode::ReadMode); I use ITK 5.1 to read …

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## [Undefined reference to image registers](https://discourse.itk.org/t/undefined-reference-to-image-registers/3717)

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**Author:** [@rohit\_inippully](https://discourse.itk.org/u/rohit_inippully)\
**Replies:** 4\
**Last updated:** [December 22, 2020, 4:05pm UTC](https://discourse.itk.org/t/undefined-reference-to-image-registers/3717 "2020-12-22T16:05:19Z")

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Hey, I am getting an error when compiling the examples given in the itk software guide. Can anyone advise me how to fix this? Thank you, Rohit Inippully.

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## [Getting error in mhd file reading](https://discourse.itk.org/t/getting-error-in-mhd-file-reading/3727)

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**Author:** [@anirban1513](https://discourse.itk.org/u/anirban1513)\
**Replies:** 1\
**Last updated:** [December 22, 2020, 1:51pm UTC](https://discourse.itk.org/t/getting-error-in-mhd-file-reading/3727 "2020-12-22T13:51:15Z")

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I am getting this error!! THE mhd File can’t be found or read by the simpleitk 1.2.4 I am getting the same error! What to do?? RuntimeError: Exception thrown in SimpleITK ReadImage: /tmp/SimpleITK-build/ITK/Modules/I…

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## [How to speed up for 3D filtering](https://discourse.itk.org/t/how-to-speed-up-for-3d-filtering/3719)

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**Author:** [@buyierfei](https://discourse.itk.org/u/buyierfei)\
**Replies:** 8\
**Last updated:** [December 21, 2020, 4:17pm UTC](https://discourse.itk.org/t/how-to-speed-up-for-3d-filtering/3719 "2020-12-21T16:17:59Z")

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I found it such slow that using built-in 3D filtering method directly. For example, I want to implement mean filtering in a 3D image data, which size is 1024 \* 1024 \* 1024, and I use itkMeanImageFilter method, but it sea…

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## [Translate ITK DeformableRegistration15.cxx into SimpleITK](https://discourse.itk.org/t/translate-itk-deformableregistration15-cxx-into-simpleitk/3691)

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**Author:** [@cdcooke](https://discourse.itk.org/u/cdcooke)\
**Replies:** 3\
**Last updated:** [December 16, 2020, 2:44pm UTC](https://discourse.itk.org/t/translate-itk-deformableregistration15-cxx-into-simpleitk/3691 "2020-12-16T14:44:41Z")

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Greetings! Has anyone tried converting the ITK DeformableRegistration15.cxx example for use with SimpleITK? There are several calls in the DeformableRegistration15.cxx that I can’t seem to map into SimpleITK. Any help…

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## [Help displaying a 3D Dicom and the corresponding segmentation Slicewise using itkwidgets](https://discourse.itk.org/t/help-displaying-a-3d-dicom-and-the-corresponding-segmentation-slicewise-using-itkwidgets/3507)

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**Author:** [@Kashyap](https://discourse.itk.org/u/Kashyap)\
**Replies:** 6\
**Last updated:** [December 15, 2020, 10:01pm UTC](https://discourse.itk.org/t/help-displaying-a-3d-dicom-and-the-corresponding-segmentation-slicewise-using-itkwidgets/3507 "2020-12-15T22:01:01Z")

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I am able to display the 3D Dicom read using simple ITK and also overlay the corresponding segmentation mesh in vtkpolydata format. Now I am trying to display the same image slice wise (kind of like an extension of the …

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## [CMake Error](https://discourse.itk.org/t/cmake-error/3705)

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**Author:** [@Afzaal786-wq](https://discourse.itk.org/u/Afzaal786-wq)\
**Replies:** 1\
**Last updated:** [December 15, 2020, 9:40pm UTC](https://discourse.itk.org/t/cmake-error/3705 "2020-12-15T21:40:16Z")

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Hello hope you doing well, I have installed ITK 5.1.2 successfully for Gate 9.0 installation. But during configuration of ITK i got this error even file ITKConfig.cmake is present in ITK5.1.2/bin. CMake Error at CMakeLi…

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## [cmpiling ITK on CentOs - pcre/swig error](https://discourse.itk.org/t/cmpiling-itk-on-centos-pcre-swig-error/3673)

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**Author:** [@Yaron](https://discourse.itk.org/u/Yaron)\
**Replies:** 5\
**Last updated:** [December 10, 2020, 9:56pm UTC](https://discourse.itk.org/t/cmpiling-itk-on-centos-pcre-swig-error/3673 "2020-12-10T21:56:59Z")

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Hello, I am trying to compile ITK on a CentOs 7 cluster. During the compilation, I get the error - \[ 56%\] Completed ‘PCRE’ \[ 56%\] Built target PCRE … \[ 56%\] No update step for ‘swig’ \[ 56%\] No patch step for ‘swig’ …

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## [creating an GPU image from a pointer](https://discourse.itk.org/t/creating-an-gpu-image-from-a-pointer/3696)

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**Author:** [@agerardin](https://discourse.itk.org/u/agerardin)\
**Replies:** 0\
**Last updated:** [December 10, 2020, 5:43pm UTC](https://discourse.itk.org/t/creating-an-gpu-image-from-a-pointer/3696 "2020-12-10T17:43:22Z")

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Is it possible to provide an existing pointer to unified memory and create a GPUImage? I am managing my data through another library but I would like to leverage some of the nice 3D processing ITK provides.

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## [How to extract the region](https://discourse.itk.org/t/how-to-extract-the-region/3687)

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**Author:** [@buyierfei](https://discourse.itk.org/u/buyierfei)\
**Replies:** 5\
**Last updated:** [December 10, 2020, 2:26pm UTC](https://discourse.itk.org/t/how-to-extract-the-region/3687 "2020-12-10T14:26:41Z")

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I am a beginner. I use the connected component analysis method to extract the labels of a volume data. How can I use any one of the labels as a mask to extract the corresponding area in the original data? Which header fi…

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## [Generalized dicom series reader](https://discourse.itk.org/t/generalized-dicom-series-reader/3692)

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**Author:** [@Hasna](https://discourse.itk.org/u/Hasna)\
**Replies:** 2\
**Last updated:** [December 10, 2020, 2:59am UTC](https://discourse.itk.org/t/generalized-dicom-series-reader/3692 "2020-12-10T02:59:56Z")

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Hi, I am trying to write a generalized reader code for dicom series. To get the component type of the data i am reading first dicom file of the series and using dicomIO-\>GetComponentType() .This will give whether the …

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## [Creating a displacement field image from a numpy array](https://discourse.itk.org/t/creating-a-displacement-field-image-from-a-numpy-array/3681)

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**Author:** [@Alex\_Reimelt](https://discourse.itk.org/u/Alex_Reimelt)\
**Replies:** 11\
**Last updated:** [December 8, 2020, 5:06pm UTC](https://discourse.itk.org/t/creating-a-displacement-field-image-from-a-numpy-array/3681 "2020-12-08T17:06:18Z")

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Hello, in my PhD project I analyze 3D microCT datasets of lung tissue samples to find out more about the alveolar shape. One topic is the simulation of an atelectasis by warping the image. In order to do that (using the…

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## [Create ITK Setup project](https://discourse.itk.org/t/create-itk-setup-project/3678)

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**Author:** [@James](https://discourse.itk.org/u/James)\
**Replies:** 3\
**Last updated:** [December 5, 2020, 6:25pm UTC](https://discourse.itk.org/t/create-itk-setup-project/3678 "2020-12-05T18:25:06Z")

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Hi, I’m new here. I downloaded ITK 5.1.1 for Windows, configured, generated using CMake successfully, and Compiled successfully on Visual Studio 2019. When I trying to create installation project got error: Building …

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## [Interpolate between slices or remove segmentation outlier](https://discourse.itk.org/t/interpolate-between-slices-or-remove-segmentation-outlier/3666)

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**Author:** [@farhan\_009](https://discourse.itk.org/u/farhan_009)\
**Replies:** 3\
**Last updated:** [December 1, 2020, 2:22pm UTC](https://discourse.itk.org/t/interpolate-between-slices-or-remove-segmentation-outlier/3666 "2020-12-01T14:22:04Z")

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Hello Everyone, I have the following output from the prediction of the deep learning model. Is there any function that interpolates the segmented result of I have to remove the dots? I have tried to use the LinearInter…

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## [How to read dicom files in two folders by SimpleITK?](https://discourse.itk.org/t/how-to-read-dicom-files-in-two-folders-by-simpleitk/3663)

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**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 2\
**Last updated:** [November 30, 2020, 4:10am UTC](https://discourse.itk.org/t/how-to-read-dicom-files-in-two-folders-by-simpleitk/3663 "2020-11-30T04:10:10Z")

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SimpleITK is a useful tool for medical image processing. It can read dicom images by: import SimpleITK as sitk series\_IDs = sitk.ImageSeriesReader.GetGDCMSeriesIDs(file\_path) series\_file\_names = sitk.ImageSeriesReade…

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## [No outputs from view(image) of itkwidgets](https://discourse.itk.org/t/no-outputs-from-view-image-of-itkwidgets/3657)

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**Author:** [@Satya](https://discourse.itk.org/u/Satya)\
**Replies:** 5\
**Last updated:** [November 28, 2020, 1:09am UTC](https://discourse.itk.org/t/no-outputs-from-view-image-of-itkwidgets/3657 "2020-11-28T01:09:30Z")

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When I run the following lines from the jupyter notebook provided as examples on github in my system, I fail to get any outputs : image = itk.imread(file\_name) view(image) I have checked everything from the package ve…

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## [Extract surface mesh from 3D binary mask images](https://discourse.itk.org/t/extract-surface-mesh-from-3d-binary-mask-images/3646)

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**Author:** [@isuruwi](https://discourse.itk.org/u/isuruwi)\
**Replies:** 1\
**Last updated:** [November 24, 2020, 4:47pm UTC](https://discourse.itk.org/t/extract-surface-mesh-from-3d-binary-mask-images/3646 "2020-11-24T16:47:15Z")

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I have generated a segmentation mask for a CT volume and and saved it as a nifti format. This image volume consists of below set of categories. 0: Background (None of the following organs) 1: Liver 2: Bladder 3: Lung…

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## [How to compare a slice and its next?](https://discourse.itk.org/t/how-to-compare-a-slice-and-its-next/3645)

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**Author:** [@Enr\_Brunetti](https://discourse.itk.org/u/Enr_Brunetti)\
**Replies:** 0\
**Last updated:** [November 23, 2020, 6:16pm UTC](https://discourse.itk.org/t/how-to-compare-a-slice-and-its-next/3645 "2020-11-23T18:16:35Z")

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I have a series of CT slice and I want to compare these ones in the axial view, because I want to delete elements in the slice, that not appear in the following slices. Is there any function in ITK or OpenCV, that can pe…

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