# Beginner Questions

**URL:** https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=24

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**Page:** 25

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## [Save itk image with custom voxel spacing](https://discourse.itk.org/t/save-itk-image-with-custom-voxel-spacing/3634)

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**Author:** [@farhan\_009](https://discourse.itk.org/u/farhan_009)\
**Replies:** 7\
**Last updated:** [November 20, 2020, 3:15am UTC](https://discourse.itk.org/t/save-itk-image-with-custom-voxel-spacing/3634 "2020-11-20T03:15:51Z")

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Hello everyone! I got output from the model which is a NumPy array of shape \[128,448,448 \] .I converted to itkobject using itk.image\_view\_from\_array(predicted\_label) and save the image with itkwrite .But shape of inpu…

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## [How can I use GetBufferAsInt64 in c#](https://discourse.itk.org/t/how-can-i-use-getbufferasint64-in-c/3623)

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**Author:** [@Anders\_G](https://discourse.itk.org/u/Anders_G)\
**Replies:** 4\
**Last updated:** [November 19, 2020, 12:15pm UTC](https://discourse.itk.org/t/how-can-i-use-getbufferasint64-in-c/3623 "2020-11-19T12:15:14Z")

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I want to access the raw data pointer of an image in simpleITK c#. (It will be sent to another native library.) I understand how to do it for types like sitkFloat32 and sitkInt32 since the GetBufferAsXXX returns a IntPtr…

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## [Using fuzzy connectedness algorithm](https://discourse.itk.org/t/using-fuzzy-connectedness-algorithm/3625)

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**Author:** [@Nayra\_Ahmed](https://discourse.itk.org/u/Nayra_Ahmed)\
**Replies:** 1\
**Last updated:** [November 16, 2020, 1:56pm UTC](https://discourse.itk.org/t/using-fuzzy-connectedness-algorithm/3625 "2020-11-16T13:56:17Z")

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Hi there, I want to use fuzzy connectedness algorithm in my project and I didn’t find it in the latest version. So how can I use it? Thanks in advance. Best Regards, Nayra

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## [How to save the coordinates of ROI for ITK-SNAP](https://discourse.itk.org/t/how-to-save-the-coordinates-of-roi-for-itk-snap/3614)

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**Author:** [@nguyenhoa93](https://discourse.itk.org/u/nguyenhoa93)\
**Replies:** 1\
**Last updated:** [November 13, 2020, 4:33pm UTC](https://discourse.itk.org/t/how-to-save-the-coordinates-of-roi-for-itk-snap/3614 "2020-11-13T16:33:20Z")

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Hello, I am using ITK-SNAP for visualization and define the bounding box of the heart region for 3D CT scans. I found that the features in Snake are so cool. ROI can help me do that easily but I can’t save the coordinat…

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## [3D registration results not consistent between two metrics](https://discourse.itk.org/t/3d-registration-results-not-consistent-between-two-metrics/3598)

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**Author:** [@Anesh](https://discourse.itk.org/u/Anesh)\
**Replies:** 6\
**Last updated:** [November 9, 2020, 4:02pm UTC](https://discourse.itk.org/t/3d-registration-results-not-consistent-between-two-metrics/3598 "2020-11-09T16:02:27Z")

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Hello, I recently started using ITKv3 for 3D registration based on ImageRegistraton8.cxx Note that ITK is interfaced to another software for image processing. For testing purpose, I started with the 3D images (brainwe…

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## [shrinkFactor causing weird artefacts with sitk.DisplacementFieldTransform](https://discourse.itk.org/t/shrinkfactor-causing-weird-artefacts-with-sitk-displacementfieldtransform/3574)

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**Author:** [@jingxuan](https://discourse.itk.org/u/jingxuan)\
**Replies:** 8\
**Last updated:** [November 7, 2020, 7:03pm UTC](https://discourse.itk.org/t/shrinkfactor-causing-weird-artefacts-with-sitk-displacementfieldtransform/3574 "2020-11-07T19:03:38Z")

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Hi everyone. I’m new to SimpleITK. It’s been great so far and I’m hoping to do more with it. I’m trying to perform a dense deformable registration between two 3D volumes, initialized with an affine registration performe…

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## [Creating an image mosaic in SimpleITK](https://discourse.itk.org/t/creating-an-image-mosaic-in-simpleitk/3582)

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**Author:** [@user1](https://discourse.itk.org/u/user1)\
**Replies:** 4\
**Last updated:** [November 6, 2020, 9:28pm UTC](https://discourse.itk.org/t/creating-an-image-mosaic-in-simpleitk/3582 "2020-11-06T21:28:07Z")

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I’m new to SimpleITK and am looking to create an image mosaic of a large number of grayscale images (probability maps from binary segmentation of blood vessels) through sequential image registration. Since I’m quite new …

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## [SimpleITK can not obtain the 0020|000D DICOM tag](https://discourse.itk.org/t/simpleitk-can-not-obtain-the-0020-000d-dicom-tag/3594)

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**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 2\
**Last updated:** [November 4, 2020, 2:22pm UTC](https://discourse.itk.org/t/simpleitk-can-not-obtain-the-0020-000d-dicom-tag/3594 "2020-11-04T14:22:16Z")

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I want to use SimpleITK to obtain the tag information, and the code is: reader = sitk.ImageFileReader() reader.SetFileName(fileName) reader.LoadPrivateTagsOn() reader.ReadImageInformation() if reade…

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## [Read gifti file written by CAT toolbox](https://discourse.itk.org/t/read-gifti-file-written-by-cat-toolbox/3588)

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**Author:** [@crossmanith](https://discourse.itk.org/u/crossmanith)\
**Replies:** 8\
**Last updated:** [November 3, 2020, 4:42pm UTC](https://discourse.itk.org/t/read-gifti-file-written-by-cat-toolbox/3588 "2020-11-03T16:42:52Z")

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Hi, I’d like to postprocess a gifti file written by the CAT toolbox (matlab). It contains one data array with scalar values, one data array with vertices and a third data array with triangles. itk::MeshFileReader offers…

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## [itkPolyLineParametricPathPython to python list](https://discourse.itk.org/t/itkpolylineparametricpathpython-to-python-list/3578)

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**Author:** [@Lee\_Newberg](https://discourse.itk.org/u/Lee_Newberg)\
**Replies:** 0\
**Last updated:** [October 28, 2020, 7:21pm UTC](https://discourse.itk.org/t/itkpolylineparametricpathpython-to-python-list/3578 "2020-10-28T19:21:26Z")

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How do I convert an itk.itkPolyLineParametricPathPython.itkPolyLineParametricPath2 object (produced by itk.contour\_extractor2\_d\_image\_filter) into a Python list of tuples or something similar?

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## [How to import ITKTwoProjectionRegistration module in python](https://discourse.itk.org/t/how-to-import-itktwoprojectionregistration-module-in-python/3576)

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**Author:** [@isuruwi](https://discourse.itk.org/u/isuruwi)\
**Replies:** 0\
**Last updated:** [October 28, 2020, 11:22am UTC](https://discourse.itk.org/t/how-to-import-itktwoprojectionregistration-module-in-python/3576 "2020-10-28T11:22:30Z")

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I have successfully installed the ITKTwoProjectionRegistration package and now I want to use SiddonJacobsRayCastInterpolateImageFunction function there. I attempted to use this functionality, but unfortunately it is not…

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## [Get Image Metadata of the whole DICOM series \[SimpleITK\]](https://discourse.itk.org/t/get-image-metadata-of-the-whole-dicom-series-simpleitk/3570)

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**Author:** [@ibro45](https://discourse.itk.org/u/ibro45)\
**Replies:** 7\
**Last updated:** [October 26, 2020, 12:32pm UTC](https://discourse.itk.org/t/get-image-metadata-of-the-whole-dicom-series-simpleitk/3570 "2020-10-26T12:32:07Z")

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Hi! Is there a way to adapt the example at Read Image Meta-Data Dictionary and Print so that it shows image metadata of the whole DICOM series? Specifically, with the above example it is possible to read a single dicom…

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## [ImageSeriesReader speed](https://discourse.itk.org/t/imageseriesreader-speed/3558)

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**Author:** [@jwitos](https://discourse.itk.org/u/jwitos)\
**Replies:** 3\
**Last updated:** [October 22, 2020, 5:55pm UTC](https://discourse.itk.org/t/imageseriesreader-speed/3558 "2020-10-22T17:55:23Z")

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Hi everyone, I’m currently using SimpleITK (2.0) ImageSeriesReader to process several hundred of MR studies. I am using the standard approach with GetGDCMSeriesIDs -\> GetGDCMSeriesFileNames -\> Execute. It is working fin…

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## [link error. ld: symbol(s) not found for architecture x86\_64](https://discourse.itk.org/t/link-error-ld-symbol-s-not-found-for-architecture-x86-64/3554)

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**Author:** [@kaiyan\_liu](https://discourse.itk.org/u/kaiyan_liu)\
**Replies:** 5\
**Last updated:** [October 22, 2020, 1:13pm UTC](https://discourse.itk.org/t/link-error-ld-symbol-s-not-found-for-architecture-x86-64/3554 "2020-10-22T13:13:22Z")

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I’m learning the examples provided by ITK(https://itk.org/ITKExamples/src/index.htm) when I’m trying the first example( Convert An itk::Image To vtkImageData)(https://itk.org/ITKExamples/src/Bridge/VtkGlue/ConvertAnitkI…

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## [Issues with CMake and ITK installation](https://discourse.itk.org/t/issues-with-cmake-and-itk-installation/3556)

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**Author:** [@Sebastian\_Quezada](https://discourse.itk.org/u/Sebastian_Quezada)\
**Replies:** 2\
**Last updated:** [October 22, 2020, 6:08am UTC](https://discourse.itk.org/t/issues-with-cmake-and-itk-installation/3556 "2020-10-22T06:08:08Z")

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Hi everyone, I’m sorry if this is too basic level question, but I’m having problems installing ITK. Probably the biggest problem of mine is that I’m unfamiliar with computer language such as compilations and the likes, …

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## [Resample volume to specific voxel spacing - SimpleITK](https://discourse.itk.org/t/resample-volume-to-specific-voxel-spacing-simpleitk/3531)

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**Author:** [@Tommaso\_Di\_Noto](https://discourse.itk.org/u/Tommaso_Di_Noto)\
**Replies:** 7\
**Last updated:** [October 20, 2020, 7:22am UTC](https://discourse.itk.org/t/resample-volume-to-specific-voxel-spacing-simpleitk/3531 "2020-10-20T07:22:49Z")

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Hi everyone! I have a series of 3D, MR volumes acquired from different scanners. I would like to resample all volumes to their median voxel size \[0.39, 0.39, 0.55\] mm. Moreover, for each volume, I also have a binary mas…

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## [Offset changes with each registration](https://discourse.itk.org/t/offset-changes-with-each-registration/3398)

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**Author:** [@Yew\_Shu\_Ning](https://discourse.itk.org/u/Yew_Shu_Ning)\
**Replies:** 10\
**Last updated:** [October 15, 2020, 9:20pm UTC](https://discourse.itk.org/t/offset-changes-with-each-registration/3398 "2020-10-15T21:20:20Z")

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Hi! I tried to register two images, using the following code: Registration framework setup. registration\_method = sitk.ImageRegistrationMethod() #Set Interpolator registration\_method.SetInterpolator(sitk.sitkLinear) #…

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## [Crop a 3D volumetric medical image](https://discourse.itk.org/t/crop-a-3d-volumetric-medical-image/3540)

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**Author:** [@DL\_Begin](https://discourse.itk.org/u/DL_Begin)\
**Replies:** 2\
**Last updated:** [October 15, 2020, 1:07pm UTC](https://discourse.itk.org/t/crop-a-3d-volumetric-medical-image/3540 "2020-10-15T13:07:41Z")

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Hello , I have two different modality images . CT and PET whole body. For each of them I want to crop the images in x and y dimension such that the background black pixels are removed. I want to get rid of black space o…

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## [3D Resampling](https://discourse.itk.org/t/3d-resampling/3522)

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**Author:** [@jwitos](https://discourse.itk.org/u/jwitos)\
**Replies:** 4\
**Last updated:** [October 13, 2020, 8:52pm UTC](https://discourse.itk.org/t/3d-resampling/3522 "2020-10-13T20:52:49Z")

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Hi everyone, I am working with a dataset that contains studies acquired in either axial or sagittal plane. I am loading the images with the ImageSeriesReader. Trying to unify the dataset, I would like to resample them t…

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## [Comparing Vector Images?](https://discourse.itk.org/t/comparing-vector-images/3517)

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**Author:** [@crocodoyle](https://discourse.itk.org/u/crocodoyle)\
**Replies:** 2\
**Last updated:** [October 8, 2020, 9:48pm UTC](https://discourse.itk.org/t/comparing-vector-images/3517 "2020-10-08T21:48:37Z")

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Hello, I have two vector images of type itk::Image\<itk::Vector\<double, 3\>\> that I am trying to compare for similarity. My first two approaches failed and I’m not sure why… First, I found the itk::Testing::ComparisonImag…

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## [Struggling to identify a coordinate from the original volume to the new resampled euler transform volume (with offset)](https://discourse.itk.org/t/struggling-to-identify-a-coordinate-from-the-original-volume-to-the-new-resampled-euler-transform-volume-with-offset/3515)

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**Author:** [@Helena](https://discourse.itk.org/u/Helena)\
**Replies:** 4\
**Last updated:** [October 7, 2020, 6:35pm UTC](https://discourse.itk.org/t/struggling-to-identify-a-coordinate-from-the-original-volume-to-the-new-resampled-euler-transform-volume-with-offset/3515 "2020-10-07T18:35:29Z")

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I have a volume that I resample using img\_center , and a transform matrix = \[0.814277854168591, 0.58047530198157, 0, -0.58047530198157, 0.814277854168591, 0, 0, 0, 1\] via euler 3d transformation. I would like to extract…

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## [How to use itk::AffineTransform::Rotate3D in python?](https://discourse.itk.org/t/how-to-use-itk-rotate3d-in-python/3503)

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**Author:** [@ghf](https://discourse.itk.org/u/ghf)\
**Replies:** 1\
**Last updated:** [October 2, 2020, 2:37pm UTC](https://discourse.itk.org/t/how-to-use-itk-rotate3d-in-python/3503 "2020-10-02T14:37:17Z")

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How to use itk::AffineTransform::Rotate3D in python?

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## [Datatype error](https://discourse.itk.org/t/datatype-error/3499)

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**Author:** [@Romy\_Meester](https://discourse.itk.org/u/Romy_Meester)\
**Replies:** 2\
**Last updated:** [October 1, 2020, 3:03pm UTC](https://discourse.itk.org/t/datatype-error/3499 "2020-10-01T15:03:38Z")

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Hello, I try to implement several filters in SITK for 3D images, but I do get an error with the Anisotropic diffusion image filter. (The Gaussian, median and curvature flow are working :slight\_smile: ) def calc\_anisot…

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## [Wiener deconvolution image filter](https://discourse.itk.org/t/wiener-deconvolution-image-filter/3498)

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**Author:** [@Romy\_Meester](https://discourse.itk.org/u/Romy_Meester)\
**Replies:** 1\
**Last updated:** [October 1, 2020, 1:34pm UTC](https://discourse.itk.org/t/wiener-deconvolution-image-filter/3498 "2020-10-01T13:34:41Z")

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Hello, I try to implement several filters in SITK for 3D images, but I do get an error with the Wiener deconvolution image filter. (The Gaussian, median and curvature flow are working :slight\_smile: ) This is my functi…

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## [adjusting two different CT images in the same position](https://discourse.itk.org/t/adjusting-two-different-ct-images-in-the-same-position/3492)

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**Author:** [@Gokce\_Guven](https://discourse.itk.org/u/Gokce_Guven)\
**Replies:** 3\
**Last updated:** [September 30, 2020, 6:45pm UTC](https://discourse.itk.org/t/adjusting-two-different-ct-images-in-the-same-position/3492 "2020-09-30T18:45:55Z")

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Hi, I have approximately hundreds of extremity CT (.mhd files) which I want to orient in 3D space such that the images would be located in the middle of the volume and palms are looking to the same direction and save th…

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## [How can i reconstruct series or sequence of 2D DICOM images into 3D reconstruction?](https://discourse.itk.org/t/how-can-i-reconstruct-series-or-sequence-of-2d-dicom-images-into-3d-reconstruction/3495)

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**Author:** [@Yuvi-416](https://discourse.itk.org/u/Yuvi-416)\
**Replies:** 3\
**Last updated:** [September 30, 2020, 4:51pm UTC](https://discourse.itk.org/t/how-can-i-reconstruct-series-or-sequence-of-2d-dicom-images-into-3d-reconstruction/3495 "2020-09-30T16:51:18Z")

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Hello there, I had a bunch of microscopy image in a .tif or a .czi extension but I manage to convert it into Dicom standard format using pydicom. Moreover, after conversion now I have a sequence of Dicom image like from…

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## [Filter a 3D image slice by slice and store results](https://discourse.itk.org/t/filter-a-3d-image-slice-by-slice-and-store-results/3484)

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**Author:** [@Elli](https://discourse.itk.org/u/Elli)\
**Replies:** 4\
**Last updated:** [September 25, 2020, 6:49pm UTC](https://discourse.itk.org/t/filter-a-3d-image-slice-by-slice-and-store-results/3484 "2020-09-25T18:49:11Z")

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Dear all, I have a 3D volume, I want to iterate over all 2D slices, apply a convolutional filter on each slice and then put them again together as a 3D volume and store this 3D volume. Somehow, I am failing to do so an…

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## [Invert a ScaleVersor3DTransform](https://discourse.itk.org/t/invert-a-scaleversor3dtransform/3483)

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**Author:** [@reox](https://discourse.itk.org/u/reox)\
**Replies:** 6\
**Last updated:** [September 25, 2020, 5:07am UTC](https://discourse.itk.org/t/invert-a-scaleversor3dtransform/3483 "2020-09-25T05:07:20Z")

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I tried to invert a ScaleVersor3DTransform, but I get this error message: \>\>\> import SimpleITK as sitk \>\>\> tx = sitk.ScaleVersor3DTransform() \>\>\> tx.SetTranslation(\[1,2,3\]) \>\>\> tx.SetScale(\[0.9, 1.1, 1.2\]) \>\>\> tx.GetInv…

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## [GetDirection and GetOrigin for SimpleITK C# implementation](https://discourse.itk.org/t/getdirection-and-getorigin-for-simpleitk-c-implementation/3472)

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**Author:** [@Guilmer](https://discourse.itk.org/u/Guilmer)\
**Replies:** 8\
**Last updated:** [September 23, 2020, 7:54pm UTC](https://discourse.itk.org/t/getdirection-and-getorigin-for-simpleitk-c-implementation/3472 "2020-09-23T19:54:16Z")

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Hi, I am using the C# implementation for SimpleITK to display MRI data in the Unity game engine and I am running into issues with orientations and IJK to world transform matrices. My data is a nifti file in RAS coordin…

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## ['itkMatrixD33' object does not support indexing](https://discourse.itk.org/t/itkmatrixd33-object-does-not-support-indexing/3479)

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**Author:** [@isuruwi](https://discourse.itk.org/u/isuruwi)\
**Replies:** 0\
**Last updated:** [September 22, 2020, 10:32am UTC](https://discourse.itk.org/t/itkmatrixd33-object-does-not-support-indexing/3479 "2020-09-22T10:32:36Z")

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I’m trying to implement the ComputeIndexToPhysicalPointMatrices functionality. I have initialized scale variable as below in python. (scale is a DirectionType variable in c++ code) scale = itk.Matrix.D33() And the tr…

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