# Beginner Questions

**URL:** https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=42

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**Page:** 43

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## [How to catch warnings during registration with simpleITK (python)](https://discourse.itk.org/t/how-to-catch-warnings-during-registration-with-simpleitk-python/501)

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**Author:** [@madanh](https://discourse.itk.org/u/madanh)\
**Replies:** 5\
**Last updated:** [December 13, 2017, 10:03am UTC](https://discourse.itk.org/t/how-to-catch-warnings-during-registration-with-simpleitk-python/501 "2017-12-13T10:03:22Z")

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I’m performing image registration with simpleITK (python) using ImageRegistrationMethod.Execute() approach. The purpose is to collect some statistics of the image registration process (e.g. find out when it succeeds an…

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## [Radius of Neighborhood Correlation](https://discourse.itk.org/t/radius-of-neighborhood-correlation/503)

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**Author:** [@Ray](https://discourse.itk.org/u/Ray)\
**Replies:** 3\
**Last updated:** [December 12, 2017, 6:01pm UTC](https://discourse.itk.org/t/radius-of-neighborhood-correlation/503 "2017-12-12T18:01:43Z")

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For the metric “ANTSNeighborhoodCorrelationImageToImageMetricv4”, we can set up the radius of the neighborhood by SetRadius(). I wonder if the radius is defined on physical space or image space? i.e. the unit is mm or vo…

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## [Inverse of BSpline transform](https://discourse.itk.org/t/inverse-of-bspline-transform/496)

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**Author:** [@Ray](https://discourse.itk.org/u/Ray)\
**Replies:** 1\
**Last updated:** [December 11, 2017, 3:52pm UTC](https://discourse.itk.org/t/inverse-of-bspline-transform/496 "2017-12-11T15:52:16Z")

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I’m using the following code to generate an inverse transform of a BSpline transform. However, no matter what my “outputTransform” is, the “inverseOutputTransform” is all zeros. Is there anything wrong of using GetInvers…

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## [Segmentation fault displaying float image](https://discourse.itk.org/t/segmentation-fault-displaying-float-image/486)

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**Author:** [@bonisthegreat](https://discourse.itk.org/u/bonisthegreat)\
**Replies:** 11\
**Last updated:** [December 9, 2017, 3:37pm UTC](https://discourse.itk.org/t/segmentation-fault-displaying-float-image/486 "2017-12-09T15:37:31Z")

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Hello there! I get a segmentation fault when trying to display or apply any filter to an ikt::Image with float pixel types. I can use this same code (swapping the pixel types) to open an image with unsigned char pixel ty…

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## [proper dir. structure for ITK installation on VS](https://discourse.itk.org/t/proper-dir-structure-for-itk-installation-on-vs/491)

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**Author:** [@siddys](https://discourse.itk.org/u/siddys)\
**Replies:** 5\
**Last updated:** [December 9, 2017, 1:05am UTC](https://discourse.itk.org/t/proper-dir-structure-for-itk-installation-on-vs/491 "2017-12-09T01:05:02Z")

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Hi everyone, I am posting as a newbie since I am using ITK on a windows environment for the first time, and due to restrictions on binary installation in my workplace, I am trying to install ITK by compiling from sourc…

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## [AffineTransform Rotate3D in Y-Axis](https://discourse.itk.org/t/affinetransform-rotate3d-in-y-axis/476)

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**Author:** [@Equis](https://discourse.itk.org/u/Equis)\
**Replies:** 5\
**Last updated:** [December 4, 2017, 2:36pm UTC](https://discourse.itk.org/t/affinetransform-rotate3d-in-y-axis/476 "2017-12-04T14:36:42Z")

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Hi: I don’t know if I am so stupid or what, but anybodu knows how to rotate a 3D DICOM 180º in the y-axis? I used AffineTransform with Rotate3D and ResampleImageFilter. I even was able to rotate 180º in the z-axis but I…

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## [ITKVTKGlue Module in Python Wheel](https://discourse.itk.org/t/itkvtkglue-module-in-python-wheel/393)

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**Author:** [@Besler](https://discourse.itk.org/u/Besler)\
**Replies:** 12\
**Last updated:** [December 2, 2017, 5:49am UTC](https://discourse.itk.org/t/itkvtkglue-module-in-python-wheel/393 "2017-12-02T05:49:58Z")

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I am trying to use ITK and VTK together in python. I installed everything through pip. Quickly trying I get the following error: $ conda create -n proc python=3 $ source activate proc $ pip install itk $ conda install …

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## [composite transform not maked as modified when using SetParameters](https://discourse.itk.org/t/composite-transform-not-maked-as-modified-when-using-setparameters/458)

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**Author:** [@asertyuio](https://discourse.itk.org/u/asertyuio)\
**Replies:** 5\
**Last updated:** [December 1, 2017, 3:27pm UTC](https://discourse.itk.org/t/composite-transform-not-maked-as-modified-when-using-setparameters/458 "2017-12-01T15:27:18Z")

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Dear all, I have a small and maybe silly question. I noticed that when I was changing manually the parameter of the last transform in a composite transform, the composite transform was not marked as modified. For examp…

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## [Single transform from composition of linear transform ?](https://discourse.itk.org/t/single-transform-from-composition-of-linear-transform/464)

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**Author:** [@asertyuio](https://discourse.itk.org/u/asertyuio)\
**Replies:** 3\
**Last updated:** [December 1, 2017, 3:02pm UTC](https://discourse.itk.org/t/single-transform-from-composition-of-linear-transform/464 "2017-12-01T15:02:11Z")

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Dear All, I have some linear transforms that are packed into a composite transform. Is there a way of calculating a single affine transform that would be the result of the composition ? I haven’t found any function to …

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## [Wrappers for ITK](https://discourse.itk.org/t/wrappers-for-itk/456)

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**Author:** [@cae2017](https://discourse.itk.org/u/cae2017)\
**Replies:** 2\
**Last updated:** [December 1, 2017, 2:08pm UTC](https://discourse.itk.org/t/wrappers-for-itk/456 "2017-12-01T14:08:23Z")

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Hello, while installing and setting up ITK, I saw that there are some pre-defined wrappers for some programming languages. Is there a way to install an extra package so that I can use C#? I fount ActiViz but it seems to…

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## [IsoVolume on RGB video frames sequence volume](https://discourse.itk.org/t/isovolume-on-rgb-video-frames-sequence-volume/474)

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**Author:** [@Joe\_Kozak](https://discourse.itk.org/u/Joe_Kozak)\
**Replies:** 1\
**Last updated:** [December 1, 2017, 1:27pm UTC](https://discourse.itk.org/t/isovolume-on-rgb-video-frames-sequence-volume/474 "2017-12-01T13:27:53Z")

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If i load a bunch of video frame jpeg into paraview, i cant use IsoVolume, why is that. Isnt each voxel just a 3 dimentional number e.g. RGB not scalar, can I not carve out a new IsoVolume based on some threshold value o…

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## [Where to find detailed definition/description of ITK classes?](https://discourse.itk.org/t/where-to-find-detailed-definition-description-of-itk-classes/460)

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**Author:** [@HsuehWen](https://discourse.itk.org/u/HsuehWen)\
**Replies:** 3\
**Last updated:** [November 29, 2017, 4:29pm UTC](https://discourse.itk.org/t/where-to-find-detailed-definition-description-of-itk-classes/460 "2017-11-29T16:29:22Z")

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Hi, I’m new to ITK and when I have questions, I usually do search on doxygen and SoftwareGuide. However, I sometimes found the information not detailed enough (at least for my curiosity :yum:). Is there any other resour…

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## [Problem calculating oriented bounding box, itk::ShapeLabelObject](https://discourse.itk.org/t/problem-calculating-oriented-bounding-box-itk-shapelabelobject/455)

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**Author:** [@Elli](https://discourse.itk.org/u/Elli)\
**Replies:** 3\
**Last updated:** [November 29, 2017, 8:43am UTC](https://discourse.itk.org/t/problem-calculating-oriented-bounding-box-itk-shapelabelobject/455 "2017-11-29T08:43:27Z")

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Dear all, I need the size of the oriented bounding box of a mask. I created a shape label object and extracted already some attributes (like nr. of pixels etc), what works pretty fine. Now I wanted to get the size of …

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## [transform center is reset to origin with composite transform during registration](https://discourse.itk.org/t/transform-center-is-reset-to-origin-with-composite-transform-during-registration/457)

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**Author:** [@asertyuio](https://discourse.itk.org/u/asertyuio)\
**Replies:** 5\
**Last updated:** [November 27, 2017, 3:20pm UTC](https://discourse.itk.org/t/transform-center-is-reset-to-origin-with-composite-transform-during-registration/457 "2017-11-27T15:20:10Z")

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Dear all, In my multilevel registration application, I’m using a specific initialization. So I just give parameters (scale rotation translation) + center to the transform being optimized (in place) before the registrat…

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## [MetaImage headers, how to get them?](https://discourse.itk.org/t/metaimage-headers-how-to-get-them/453)

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**Author:** [@cae2017](https://discourse.itk.org/u/cae2017)\
**Replies:** 3\
**Last updated:** [November 23, 2017, 2:57pm UTC](https://discourse.itk.org/t/metaimage-headers-how-to-get-them/453 "2017-11-23T14:57:10Z")

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Hi, I’m really new working with ITK and VTK and I’d really appreciate a little help. I’m trying out the examples available online and I’ve seen that I need a \*.mha or \*.mhd file. My question is, is it possible to get th…

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## [Extracting vectors from displacement field](https://discourse.itk.org/t/extracting-vectors-from-displacement-field/417)

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**Author:** [@thanos](https://discourse.itk.org/u/thanos)\
**Replies:** 1\
**Last updated:** [November 16, 2017, 8:59pm UTC](https://discourse.itk.org/t/extracting-vectors-from-displacement-field/417 "2017-11-16T20:59:05Z")

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Hello everyone, I am performing volume registration and so far I was using ParaView and Glyphs to visualize the deformation field (after saving it in .vtk format). I am wondering though, if there is a way to extract th…

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## [Root Mean Square Surface Distance - Mauerer Distances Map. how to calculate it?](https://discourse.itk.org/t/root-mean-square-surface-distance-mauerer-distances-map-how-to-calculate-it/424)

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**Author:** [@ral\_san](https://discourse.itk.org/u/ral_san)\
**Replies:** 1\
**Last updated:** [November 15, 2017, 6:15pm UTC](https://discourse.itk.org/t/root-mean-square-surface-distance-mauerer-distances-map-how-to-calculate-it/424 "2017-11-15T18:15:19Z")

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Below it’s my code for trying to calculate the symmetric root mean square distance. But I am not getting the right values. I can’t figure out where is the mistake in my approach. segmented\_surface\_mask = sitk.LabelCont…

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## [Problems with deformation functions](https://discourse.itk.org/t/problems-with-deformation-functions/378)

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**Author:** [@Micholas](https://discourse.itk.org/u/Micholas)\
**Replies:** 11\
**Last updated:** [November 9, 2017, 4:16pm UTC](https://discourse.itk.org/t/problems-with-deformation-functions/378 "2017-11-09T16:16:47Z")

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Hello ! I’m a beginner with ITK… What I really need is to use the Laplacian Deformation for an object. However, I don’t really understand how to do that stuff. Is there any example I can get or any guidelines because I’…

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## [How to get PixelType from Image](https://discourse.itk.org/t/how-to-get-pixeltype-from-image/374)

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**Author:** [@benjaminhon](https://discourse.itk.org/u/benjaminhon)\
**Replies:** 5\
**Last updated:** [November 8, 2017, 5:54pm UTC](https://discourse.itk.org/t/how-to-get-pixeltype-from-image/374 "2017-11-08T17:54:57Z")

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Hi is it possible to get the Pixel type from an ITK Image? It seems like Simple ITK has GetPixelDValue. I can’t find any examples of how to do this is ITK though. Thanks, Benjamin

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## [itk imageToVTKImageFilter does not seem to update vtkImageViewer2](https://discourse.itk.org/t/itk-imagetovtkimagefilter-does-not-seem-to-update-vtkimageviewer2/395)

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**Author:** [@benjaminhon](https://discourse.itk.org/u/benjaminhon)\
**Replies:** 5\
**Last updated:** [November 8, 2017, 2:01pm UTC](https://discourse.itk.org/t/itk-imagetovtkimagefilter-does-not-seem-to-update-vtkimageviewer2/395 "2017-11-08T14:01:25Z")

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Hi I have a pipeline as follows: itkReader -\> itkThreshold -\> itkImageToVTKImageFilter -\> vtkImageViewer2 im using SetInput, GetOutput to connect the pipeline. However, when I change the threshold parameters, and call …

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## [Using LabelMap in Python](https://discourse.itk.org/t/using-labelmap-in-python/259)

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**Author:** [@fbudin](https://discourse.itk.org/u/fbudin)\
**Replies:** 4\
**Last updated:** [November 3, 2017, 8:38pm UTC](https://discourse.itk.org/t/using-labelmap-in-python/259 "2017-11-03T20:38:24Z")

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The ITK example to show how to use itk.LabelMapOverlayImageFilter is only written in C++. This post show how to find types that are available in Python for a specific ITK filter and in the case of itk.LabelMap, who to i…

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## [itk.ApproximateSignedDistanceMapImageFilter error](https://discourse.itk.org/t/itk-approximatesigneddistancemapimagefilter-error/361)

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**Author:** [@mafuentes](https://discourse.itk.org/u/mafuentes)\
**Replies:** 3\
**Last updated:** [October 27, 2017, 4:29pm UTC](https://discourse.itk.org/t/itk-approximatesigneddistancemapimagefilter-error/361 "2017-10-27T16:29:15Z")

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I am using the ITK python wheels and was doing a survey of the DistanceMap filters. While trying the ApproximateSignedDistanceMapImageFilter I got an error. Sample code and error below, can anyone give me a hint as to wh…

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## [Inputs physical space do not match when using itk.LabelMapOverlayImageFilter](https://discourse.itk.org/t/inputs-physical-space-do-not-match-when-using-itk-labelmapoverlayimagefilter/272)

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**Author:** [@benjaminhon](https://discourse.itk.org/u/benjaminhon)\
**Replies:** 2\
**Last updated:** [October 10, 2017, 1:12pm UTC](https://discourse.itk.org/t/inputs-physical-space-do-not-match-when-using-itk-labelmapoverlayimagefilter/272 "2017-10-10T13:12:51Z")

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Hi, I have a DICOM Series which I loaded as well as a series of PNG files which are the segmentations. I am trying to overlay, the segmentations on top of the DICOM series, however I get this error when I do: itk.GetAr…

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## [ITKNumpyBridge problems converting from numpy array.](https://discourse.itk.org/t/itknumpybridge-problems-converting-from-numpy-array/222)

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**Author:** [@phcerdan](https://discourse.itk.org/u/phcerdan)\
**Replies:** 2\
**Last updated:** [September 27, 2017, 6:22pm UTC](https://discourse.itk.org/t/itknumpybridge-problems-converting-from-numpy-array/222 "2017-09-27T18:22:20Z")

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I am using ITKBridgeNumPy to pass an image to a numpy algorithm, and then returning it to another image. #image is a RealImageType X = itk.GetArrayViewFromImage(image) print("X", X.shape) lam = 0.1 F…

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## [Code Examples and Demo Programs](https://discourse.itk.org/t/code-examples-and-demo-programs/42)

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**Author:** [@hjmjohnson](https://discourse.itk.org/u/hjmjohnson)\
**Replies:** 1\
**Last updated:** [September 21, 2017, 11:16pm UTC](https://discourse.itk.org/t/code-examples-and-demo-programs/42 "2017-09-21T23:16:41Z")

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I am just getting started, are there any code examples that can show me how to do basic tasks?

[Previous page](https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=41)