# Beginner Questions

**URL:** https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=17

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**Page:** 18

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## [Difficulty using Rigid2DTransform in python registration demo](https://discourse.itk.org/t/difficulty-using-rigid2dtransform-in-python-registration-demo/4777)

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**Author:** [@Chris\_Roat](https://discourse.itk.org/u/Chris_Roat)\
**Replies:** 1\
**Last updated:** [February 2, 2022, 4:31pm UTC](https://discourse.itk.org/t/difficulty-using-rigid2dtransform-in-python-registration-demo/4777 "2022-02-02T16:31:30Z")

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Description I have not been able to successfully alter the translation-based python registration example to use rigid-2d-based translation (adding just a rotation angle). Steps to Reproduce Verify the unmodified demo w…

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## [3D image registration with Python and without SimpleITK](https://discourse.itk.org/t/3d-image-registration-with-python-and-without-simpleitk/4773)

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**Author:** [@edgar](https://discourse.itk.org/u/edgar)\
**Replies:** 2\
**Last updated:** [February 2, 2022, 12:04am UTC](https://discourse.itk.org/t/3d-image-registration-with-python-and-without-simpleitk/4773 "2022-02-02T00:04:07Z")

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How can I run a registration with 3D data? or what is the data type that I need and how do I input it? Thanks. Preamble Hi, firstly, I read the guidelines, and it mentioned something about “Reply as a Linked Topic”, but…

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## [Adjusting Spacing before Registration?](https://discourse.itk.org/t/adjusting-spacing-before-registration/4754)

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**Author:** [@miaomiaomiao](https://discourse.itk.org/u/miaomiaomiao)\
**Replies:** 2\
**Last updated:** [January 24, 2022, 9:13pm UTC](https://discourse.itk.org/t/adjusting-spacing-before-registration/4754 "2022-01-24T21:13:08Z")

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Hi everyone, In every I example found on the net (including the examples, which Simple ITK provides), registration is done without adjusting the spacing before. Why not first adjust the spacing and then do the registrat…

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## [when program run reader-\>update,vs throws a microsoft c++ error](https://discourse.itk.org/t/when-program-run-reader-update-vs-throws-a-microsoft-c-error/4744)

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**Author:** [@Bugmaker](https://discourse.itk.org/u/Bugmaker)\
**Replies:** 1\
**Last updated:** [January 21, 2022, 5:38pm UTC](https://discourse.itk.org/t/when-program-run-reader-update-vs-throws-a-microsoft-c-error/4744 "2022-01-21T17:38:56Z")

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i want to load a ‘nii.gz’ 3d file , but when program pass reader-\>update() ,vs2017 will give me a microsoft c++ error : Microsoft C++ 异常: itk::ImageFileReaderException，位于内存位置 0x00000000002CF0F8 处。 here is my code usin…

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## [How to use PyImageFilter](https://discourse.itk.org/t/how-to-use-pyimagefilter/4593)

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**Author:** [@jtduda](https://discourse.itk.org/u/jtduda)\
**Replies:** 2\
**Last updated:** [January 20, 2022, 11:16pm UTC](https://discourse.itk.org/t/how-to-use-pyimagefilter/4593 "2022-01-20T23:16:07Z")

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Is there a working example of how to use the itk.PyImageFilter class? It seems like the key is using the SetPyGenerateData method to set a python function to do the work. I have the below toy example working, but I can’t…

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## [How to convert DICOM file series to nrrd](https://discourse.itk.org/t/how-to-convert-dicom-file-series-to-nrrd/4561)

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**Author:** [@nyuszi](https://discourse.itk.org/u/nyuszi)\
**Replies:** 6\
**Last updated:** [January 20, 2022, 9:51pm UTC](https://discourse.itk.org/t/how-to-convert-dicom-file-series-to-nrrd/4561 "2022-01-20T21:51:46Z")

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Hello guys. I am a beginner. I use itk.js in front-end（JavaScript）. I can read DICOM files in my program the problem is that i don’t know how to convert it to nrrd. Currently It’s an array that i made with readImageDIC…

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## [Is it possible to convert/cast a .NET SimpleITK Image to python SimpleITK Image](https://discourse.itk.org/t/is-it-possible-to-convert-cast-a-net-simpleitk-image-to-python-simpleitk-image/4728)

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**Author:** [@Ervis](https://discourse.itk.org/u/Ervis)\
**Replies:** 5\
**Last updated:** [January 14, 2022, 6:13pm UTC](https://discourse.itk.org/t/is-it-possible-to-convert-cast-a-net-simpleitk-image-to-python-simpleitk-image/4728 "2022-01-14T18:13:33Z")

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Is it possible to convert/cast a .NET SimpleITK Image to python SimpleITK Image ? Has anyone successfully fused .NET c# SimpleITK images to python. I have the main application in .NET where I use SimpleITK to perform …

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## [How to hide the shadow between 2 fused/blend tiles](https://discourse.itk.org/t/how-to-hide-the-shadow-between-2-fused-blend-tiles/4725)

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**Author:** [@allen](https://discourse.itk.org/u/allen)\
**Replies:** 3\
**Last updated:** [January 12, 2022, 6:59pm UTC](https://discourse.itk.org/t/how-to-hide-the-shadow-between-2-fused-blend-tiles/4725 "2022-01-12T18:59:26Z")

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hello, im running the sample replaced the origin data with my local tiles environment: windows 10 python 3.9.0 itk-montage 0.7.3 the result seems good yet there are shadow between each tiles, is there any param in Ti…

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## [ERROR: Pixel type: vector of 8-bit signed integer is not supported](https://discourse.itk.org/t/error-pixel-type-vector-of-8-bit-signed-integer-is-not-supported/4716)

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**Author:** [@zandarina](https://discourse.itk.org/u/zandarina)\
**Replies:** 1\
**Last updated:** [January 11, 2022, 11:04am UTC](https://discourse.itk.org/t/error-pixel-type-vector-of-8-bit-signed-integer-is-not-supported/4716 "2022-01-11T11:04:08Z")

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Dear all, I write because I got this error and i have tried all types but it returns an error with whatever casting I do in the image. Exception thrown in SimpleITK LabelStatisticsImageFilter\_Execute: d:\\a\\1\\sitk\\code\\…

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## [ResampleImage for 4D data](https://discourse.itk.org/t/resampleimage-for-4d-data/4710)

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**Author:** [@Prathamesh\_Chopade](https://discourse.itk.org/u/Prathamesh_Chopade)\
**Replies:** 3\
**Last updated:** [January 6, 2022, 2:19pm UTC](https://discourse.itk.org/t/resampleimage-for-4d-data/4710 "2022-01-06T14:19:08Z")

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My goal is to upsample datasets (both 3D and 4D). ResampleImage was able to upsample 3D data, but gave an error when i tried upsampling 4D data. \*\*Are there any solutions or alternatives for this?? \*\* The command i use…

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## [Read a JPEG series](https://discourse.itk.org/t/read-a-jpeg-series/4704)

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**Author:** [@gopinath\_balaji](https://discourse.itk.org/u/gopinath_balaji)\
**Replies:** 1\
**Last updated:** [January 4, 2022, 8:35pm UTC](https://discourse.itk.org/t/read-a-jpeg-series/4704 "2022-01-04T20:35:02Z")

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Hey, I am working on Bias correction for MRI .jpg images, but I am having trouble loading in the data. I read that stik.ReadImage() accepts a string location as input but that isn’t working. Passing the image as a vari…

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## [Create image after numpy transpose](https://discourse.itk.org/t/create-image-after-numpy-transpose/3241)

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**Author:** [@emilljungberg](https://discourse.itk.org/u/emilljungberg)\
**Replies:** 2\
**Last updated:** [December 30, 2021, 7:11am UTC](https://discourse.itk.org/t/create-image-after-numpy-transpose/3241 "2021-12-30T07:11:22Z")

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Hi! I’m building an image registration framework for MRI data that requires combination of numpy and ITK. I recently realised that the indexing in ITK arrays and numpy arrays are swapped from \[x,y,z\] to \[z,y,x\] (from th…

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## [How to tune registration](https://discourse.itk.org/t/how-to-tune-registration/4707)

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**Author:** [@wangjun456](https://discourse.itk.org/u/wangjun456)\
**Replies:** 3\
**Last updated:** [December 30, 2021, 6:14am UTC](https://discourse.itk.org/t/how-to-tune-registration/4707 "2021-12-30T06:14:56Z")

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a The result seems very unsatisfactory，and my weight adjustment has no effect on the result

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## [Registering a Projective Transformed Image](https://discourse.itk.org/t/registering-a-projective-transformed-image/4695)

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**Author:** [@WhaSukGo](https://discourse.itk.org/u/WhaSukGo)\
**Replies:** 1\
**Last updated:** [December 23, 2021, 2:08pm UTC](https://discourse.itk.org/t/registering-a-projective-transformed-image/4695 "2021-12-23T14:08:25Z")

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I’m trying to register a frame from camera to a template. The most naive approach would be a feature based approach, finding a homography. Unfortunately, for my case, images don’t have adequate features to use as featu…

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## [How to create SimpleITK Image from a dicom dataset](https://discourse.itk.org/t/how-to-create-simpleitk-image-from-a-dicom-dataset/4692)

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**Author:** [@Ervis](https://discourse.itk.org/u/Ervis)\
**Replies:** 4\
**Last updated:** [December 21, 2021, 5:06pm UTC](https://discourse.itk.org/t/how-to-create-simpleitk-image-from-a-dicom-dataset/4692 "2021-12-21T17:06:54Z")

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Hi Is there a way to create/form/load a SimpleITK image / volume from a dicom dataset ? Essentially I need to load the dicom data received from a dicom node post QueryRetrieve. But instead of storing the data on disk o…

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## [create coronal images for different slice thickness of axial image](https://discourse.itk.org/t/create-coronal-images-for-different-slice-thickness-of-axial-image/4658)

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**Author:** [@gayathri](https://discourse.itk.org/u/gayathri)\
**Replies:** 8\
**Last updated:** [December 16, 2021, 2:20pm UTC](https://discourse.itk.org/t/create-coronal-images-for-different-slice-thickness-of-axial-image/4658 "2021-12-16T14:20:52Z")

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How to create coronal and sagittal images for different slice thickness

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## [Interpolate between VersorRigid3DTransforms (with different centers of rotation)](https://discourse.itk.org/t/interpolate-between-versorrigid3dtransforms-with-different-centers-of-rotation/4655)

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**Author:** [@dperl](https://discourse.itk.org/u/dperl)\
**Replies:** 7\
**Last updated:** [December 13, 2021, 7:26pm UTC](https://discourse.itk.org/t/interpolate-between-versorrigid3dtransforms-with-different-centers-of-rotation/4655 "2021-12-13T19:26:02Z")

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I want to rigidly register two very large microCT volumes (~1000x1000x1000 voxels) of a material sample taken at different times. The sample has small features (eg. roughly 10x10x10 voids), homogeneously distributed acro…

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## [python hints/autocompletion in IDE](https://discourse.itk.org/t/python-hints-autocompletion-in-ide/4670)

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**Author:** [@Gabriele\_Belotti](https://discourse.itk.org/u/Gabriele_Belotti)\
**Replies:** 4\
**Last updated:** [December 13, 2021, 4:19pm UTC](https://discourse.itk.org/t/python-hints-autocompletion-in-ide/4670 "2021-12-13T16:19:59Z")

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Hi everyone, i managed to build itk with python wrappers on a win10 machine using visual studio 2017. However I am not getting the full hints after importing itk in a visual studio code IDE. I built master at ENH: Gener…

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## [Eigen Values extraction in Python](https://discourse.itk.org/t/eigen-values-extraction-in-python/3035)

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**Author:** [@juccapirama](https://discourse.itk.org/u/juccapirama)\
**Replies:** 7\
**Last updated:** [December 9, 2021, 8:21pm UTC](https://discourse.itk.org/t/eigen-values-extraction-in-python/3035 "2021-12-09T20:21:47Z")

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Hey, I’m trying to extract the eigen values of a Hessian Image using itk.SymmetricEigenAnalysisImageFilter to further implement different vesselness filters. But the problem is that i couldn’t manipulate the result from…

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## [Problem by registration of an MRI Head image and an CT Head Image](https://discourse.itk.org/t/problem-by-registration-of-an-mri-head-image-and-an-ct-head-image/4641)

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**Author:** [@sunshine123](https://discourse.itk.org/u/sunshine123)\
**Replies:** 8\
**Last updated:** [December 8, 2021, 8:19pm UTC](https://discourse.itk.org/t/problem-by-registration-of-an-mri-head-image-and-an-ct-head-image/4641 "2021-12-08T20:19:37Z")

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Hello, I am new to image registration and I want to register an MRI Head Image with a CT image. I began with the example from this Topic to understand how image registration is working in SITK: But when I applied the…

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## [Projecting 3D points onto the DRR image plane](https://discourse.itk.org/t/projecting-3d-points-onto-the-drr-image-plane/3430)

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**Author:** [@isuruwi](https://discourse.itk.org/u/isuruwi)\
**Replies:** 40\
**Last updated:** [December 8, 2021, 3:37pm UTC](https://discourse.itk.org/t/projecting-3d-points-onto-the-drr-image-plane/3430 "2021-12-08T15:37:43Z")

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I have created a volumetric mesh. I want to get the corresponding 2D projection coordinate (i.e. x, y positions) of each vertex coordinate on the DRR image projection plane. I went through the GetDRRSiddonJacobsRayTraci…

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## [LBFGS2 optimizer missing from python](https://discourse.itk.org/t/lbfgs2-optimizer-missing-from-python/4648)

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**Author:** [@matthew.andrew17](https://discourse.itk.org/u/matthew.andrew17)\
**Replies:** 1\
**Last updated:** [December 8, 2021, 3:36pm UTC](https://discourse.itk.org/t/lbfgs2-optimizer-missing-from-python/4648 "2021-12-08T15:36:05Z")

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The LBFGS2 optimizer seems to be missing from the python pip install - from the docs there should be a couple of classes (which are available in simpleITK) - LBFGS2Optimizerv4Enums and LBFGS2Optimizerv4Template. Only LBF…

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## [Sitk.ReadImage Supported Types](https://discourse.itk.org/t/sitk-readimage-supported-types/4645)

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**Author:** [@Furkan\_Gokhan](https://discourse.itk.org/u/Furkan_Gokhan)\
**Replies:** 1\
**Last updated:** [December 7, 2021, 2:21pm UTC](https://discourse.itk.org/t/sitk-readimage-supported-types/4645 "2021-12-07T14:21:49Z")

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Hello everyone, I am using SimpleITK library for reading MRA images. For example we are work on dcm and nii file and this can be work with Sitk.ReadImage but I dont know in the future that What file types can we encou…

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## [Is it possible to compute 2D Hessian value for each slice in a 3D medical array?](https://discourse.itk.org/t/is-it-possible-to-compute-2d-hessian-value-for-each-slice-in-a-3d-medical-array/4565)

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**Author:** [@Fivethousand](https://discourse.itk.org/u/Fivethousand)\
**Replies:** 2\
**Last updated:** [November 11, 2021, 2:12pm UTC](https://discourse.itk.org/t/is-it-possible-to-compute-2d-hessian-value-for-each-slice-in-a-3d-medical-array/4565 "2021-11-11T14:12:41Z")

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Hi, I am trying to compute 2-dimention hessian value for each slice in a 3D array. I succeed computing 3D hessian value for a 3D image or 2D hessian value for a single slice by using itk.MultiScaleHessianBasedMeasureIma…

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## [Pipeline confusion?](https://discourse.itk.org/t/pipeline-confusion/4594)

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**Author:** [@Theoretialperson](https://discourse.itk.org/u/Theoretialperson)\
**Replies:** 8\
**Last updated:** [December 1, 2021, 3:38pm UTC](https://discourse.itk.org/t/pipeline-confusion/4594 "2021-12-01T15:38:28Z")

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I’m having facing a problem that possibly stems for a misunderstanding of how pipelines work and get updated. I have the following piece of code, labelfile = labelfilelist\[0\] …

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## [Orientation convention in dcm and nifti](https://discourse.itk.org/t/orientation-convention-in-dcm-and-nifti/4621)

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**Author:** [@BayesianMonk](https://discourse.itk.org/u/BayesianMonk)\
**Replies:** 3\
**Last updated:** [November 30, 2021, 3:00pm UTC](https://discourse.itk.org/t/orientation-convention-in-dcm-and-nifti/4621 "2021-11-30T15:00:41Z")

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Hi everyone, I am looking for the orientation convention in nifti and dicom. It is well known that in axial, nifti uses the RAS orientation, while dicom uses LPS orientation. But what about coronal and sagittal orient…

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## [AttributeError: module'itk' has no attribute'GradientDifferenceImageToImageMetric'](https://discourse.itk.org/t/attributeerror-moduleitk-has-no-attributegradientdifferenceimagetoimagemetric/4617)

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**Author:** [@seika](https://discourse.itk.org/u/seika)\
**Replies:** 2\
**Last updated:** [November 29, 2021, 5:49am UTC](https://discourse.itk.org/t/attributeerror-moduleitk-has-no-attributegradientdifferenceimagetoimagemetric/4617 "2021-11-29T05:49:13Z")

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When I use itk’s GradientDifferenceImageToImageMetric in a python environment, the above error occurred. Then I did not find the itkGradientDifferenceImageToImageMetricpython.py file in the packages directory. Why does…

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## [Warning with LBFGSB: does not support scaling](https://discourse.itk.org/t/warning-with-lbfgsb-does-not-support-scaling/4614)

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**Author:** [@reox](https://discourse.itk.org/u/reox)\
**Replies:** 2\
**Last updated:** [November 26, 2021, 1:52pm UTC](https://discourse.itk.org/t/warning-with-lbfgsb-does-not-support-scaling/4614 "2021-11-26T13:52:59Z")

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Here is a very simple example of an image registration: import SimpleITK as sitk x = sitk.Image(50, 50, sitk.sitkFloat32) x\[10:40,10:40\] = 1 y = sitk.Image(50, 50, sitk.sitkFloat32) y\[15:45,15:45\] = 1 sitk.ProcessObje…

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## [Multiply a vector image with scalar (SimpleITK)](https://discourse.itk.org/t/multiply-a-vector-image-with-scalar-simpleitk/4612)

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**Author:** [@Alsurayhi](https://discourse.itk.org/u/Alsurayhi)\
**Replies:** 2\
**Last updated:** [November 25, 2021, 6:19pm UTC](https://discourse.itk.org/t/multiply-a-vector-image-with-scalar-simpleitk/4612 "2021-11-25T18:19:57Z")

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To multiply a vector image with a scalar, I used import SimpleITK as sitk multiply = sitk.MultiplyImageFilter() multplied\_img = multiply.Execute(img , 0.5) my input image is of size 512 \*512 \*200 \*3. But it gives …

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## [How does ConstantPadImageFilter work](https://discourse.itk.org/t/how-does-constantpadimagefilter-work/4592)

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**Author:** [@Theoretialperson](https://discourse.itk.org/u/Theoretialperson)\
**Replies:** 7\
**Last updated:** [November 19, 2021, 2:26pm UTC](https://discourse.itk.org/t/how-does-constantpadimagefilter-work/4592 "2021-11-19T14:26:14Z")

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Can someone help me understand how ITK’s ConstantPadImageFilter works? I was expecting to get an image with slightly different origin and the same spacing when padding: pad\_filter = itk.ConstantPadImageFilter\[ImageType,…

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