# Beginner Questions

**URL:** https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=19

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

**Page:** 20

---

## [How to associate Patient, Study, Series in DICOM file information in C++ itk programming?](https://discourse.itk.org/t/how-to-associate-patient-study-series-in-dicom-file-information-in-c-itk-programming/4452)

<div class="topic-metadata">

**Author:** [@OrangeJuice3211](https://discourse.itk.org/u/OrangeJuice3211)\
**Replies:** 4\
**Last updated:** [September 28, 2021, 1:05am UTC](https://discourse.itk.org/t/how-to-associate-patient-study-series-in-dicom-file-information-in-c-itk-programming/4452 "2021-09-28T01:05:23Z")

</div>

Hello， I need to read in all Dicom files under the path that I input to get the relationship between Patient, Study and Series. But I can only get all the Tag information by reading a single DCIOM or reading DICOM serie…

---

## [How to read series of Dicom images into Django using ITK.js for web volume rendering using VTK.js?](https://discourse.itk.org/t/how-to-read-series-of-dicom-images-into-django-using-itk-js-for-web-volume-rendering-using-vtk-js/4420)

<div class="topic-metadata">

**Author:** [@Yuvi-416](https://discourse.itk.org/u/Yuvi-416)\
**Replies:** 4\
**Last updated:** [September 27, 2021, 3:28pm UTC](https://discourse.itk.org/t/how-to-read-series-of-dicom-images-into-django-using-itk-js-for-web-volume-rendering-using-vtk-js/4420 "2021-09-27T15:28:24Z")

</div>

Hello everyone, I want to load series of DICOM images into the server and want to visualize it as a volume rendering using vtk.js on the web. As I found here (https://discourse.vtk.org/t/request-hundreds-images-by-http/…

---

## [How to obtain the Hu value of DICOM in ITK in C++ programming](https://discourse.itk.org/t/how-to-obtain-the-hu-value-of-dicom-in-itk-in-c-programming/4449)

<div class="topic-metadata">

**Author:** [@sunrise](https://discourse.itk.org/u/sunrise)\
**Replies:** 3\
**Last updated:** [September 26, 2021, 11:26am UTC](https://discourse.itk.org/t/how-to-obtain-the-hu-value-of-dicom-in-itk-in-c-programming/4449 "2021-09-26T11:26:23Z")

</div>

I can get the pixel value by converteing DICOM to mat through OpenCVImageBridge, but I would have some trouble when adjusting the window width and window center. I don’t know whether you have a method that we can obtain …

---

## [Transforming Point not working when flipping](https://discourse.itk.org/t/transforming-point-not-working-when-flipping/4446)

<div class="topic-metadata">

**Author:** [@kleingeo](https://discourse.itk.org/u/kleingeo)\
**Replies:** 4\
**Last updated:** [September 24, 2021, 12:22pm UTC](https://discourse.itk.org/t/transforming-point-not-working-when-flipping/4446 "2021-09-24T12:22:50Z")

</div>

I am working on a data augmentation pipeline with a translations, rotation, scaling, flipping, and elastic deformation. I need to track how landmarks are modified during the transformation and resampling process, but the…

---

## [How could I get the TP, FP, FN, TN?](https://discourse.itk.org/t/how-could-i-get-the-tp-fp-fn-tn/1936)

<div class="topic-metadata">

**Author:** [@hubutui](https://discourse.itk.org/u/hubutui)\
**Replies:** 3\
**Last updated:** [September 24, 2021, 8:25am UTC](https://discourse.itk.org/t/how-could-i-get-the-tp-fp-fn-tn/1936 "2021-09-24T08:25:14Z")

</div>

I’m trying to evaluate my segmentation result. I could use sitk.LabelOverlapMeasuresImageFilter to get dice, FPR, FNR. I wonder if there any filter for calculating confusion matrix so that I could calcalate every metric …

---

## [ITK issue, HDF5 CXX compiler wrapper, ANTs installation](https://discourse.itk.org/t/itk-issue-hdf5-cxx-compiler-wrapper-ants-installation/4439)

<div class="topic-metadata">

**Author:** [@Surendra\_Maharjan](https://discourse.itk.org/u/Surendra_Maharjan)\
**Replies:** 1\
**Last updated:** [September 22, 2021, 9:54pm UTC](https://discourse.itk.org/t/itk-issue-hdf5-cxx-compiler-wrapper-ants-installation/4439 "2021-09-22T21:54:15Z")

</div>

Hello ITKers, My name is Suren. I am having an issue while installing ANTs in Mac Big Sur. It says "HDF5 CXX compiler wrapper is unable to compile a minimal HDF5 program. “HDF5 C compiler wrapper is unable to compile …

---

## [mask during image registration](https://discourse.itk.org/t/mask-during-image-registration/4413)

<div class="topic-metadata">

**Author:** [@Anesh](https://discourse.itk.org/u/Anesh)\
**Replies:** 2\
**Last updated:** [September 21, 2021, 2:32pm UTC](https://discourse.itk.org/t/mask-during-image-registration/4413 "2021-09-21T14:32:54Z")

</div>

Hi All, I have a basic question on registration using spatial object mask. Let’s say I have an image where the background is zero or close to zero and my mask is all ones, as illustrated below. When I run registration, …

---

## [M\_ReadElementsData: data not read completelyideal = 5734400 : actual = 2700286M](https://discourse.itk.org/t/m-readelementsdata-data-not-read-completelyideal-5734400-actual-2700286m/4424)

<div class="topic-metadata">

**Author:** [@Will\_G](https://discourse.itk.org/u/Will_G)\
**Replies:** 5\
**Last updated:** [September 15, 2021, 3:23pm UTC](https://discourse.itk.org/t/m-readelementsdata-data-not-read-completelyideal-5734400-actual-2700286m/4424 "2021-09-15T15:23:22Z")

</div>

Hi, I’m very new to using simpleITK for image conversion, my model now seemingly runs but with this one error message been presented. M\_ReadElementsData: data not read completelyideal = 5734400 : actual = 2700286 Has a…

---

## [Understanding sitk.Euler3DTransform convention](https://discourse.itk.org/t/understanding-sitk-euler3dtransform-convention/4422)

<div class="topic-metadata">

**Author:** [@MMdeB](https://discourse.itk.org/u/MMdeB)\
**Replies:** 1\
**Last updated:** [September 15, 2021, 1:20pm UTC](https://discourse.itk.org/t/understanding-sitk-euler3dtransform-convention/4422 "2021-09-15T13:20:35Z")

</div>

Hi, I’m using sitk.Euler3DTransform to rotate my 3D image, but I am confused regarding which euler convention is used. I found that sitk.Euler3DTransform uses the ZXY or ZYX convention. However, is this using extrinsic…

---

## [Unexpected Results for "MultiResImageRegistration1.cxx."](https://discourse.itk.org/t/unexpected-results-for-multiresimageregistration1-cxx/4411)

<div class="topic-metadata">

**Author:** [@Keyn34](https://discourse.itk.org/u/Keyn34)\
**Replies:** 2\
**Last updated:** [September 13, 2021, 7:49am UTC](https://discourse.itk.org/t/unexpected-results-for-multiresimageregistration1-cxx/4411 "2021-09-13T07:49:03Z")

</div>

Hello everyone! I just started out with ITK, with base knowledge from VTK. I wanted to work through some Registration examples towards Multi-Resolution Registration. The Hello World Registration example worked for me, …

---

## [Detailed description of statistics available in SimpleITK LabelShapeStatisticsImageFilter?](https://discourse.itk.org/t/detailed-description-of-statistics-available-in-simpleitk-labelshapestatisticsimagefilter/4405)

<div class="topic-metadata">

**Author:** [@jni](https://discourse.itk.org/u/jni)\
**Replies:** 2\
**Last updated:** [September 9, 2021, 12:39pm UTC](https://discourse.itk.org/t/detailed-description-of-statistics-available-in-simpleitk-labelshapestatisticsimagefilter/4405 "2021-09-09T12:39:32Z")

</div>

Hi everyone, Is there any place that lists what each of the available stats in LabelShapeStatisticsImageFilter is actually computing? My searching for what “flatness” is has taken me here: https://simpleitk.org/SPIE201…

---

## [SimpleITK Euler3D Transform, Adjust Image Origin and Direction](https://discourse.itk.org/t/simpleitk-euler3d-transform-adjust-image-origin-and-direction/3966)

<div class="topic-metadata">

**Author:** [@Nick\_Rubert](https://discourse.itk.org/u/Nick_Rubert)\
**Replies:** 24\
**Last updated:** [September 8, 2021, 2:39pm UTC](https://discourse.itk.org/t/simpleitk-euler3d-transform-adjust-image-origin-and-direction/3966 "2021-09-08T14:39:21Z")

</div>

Hi board, I have a 3D volume that I registered to another volume with ITK’s registration methods. My moving-\>fixed transformation is an Euler3DTransform. I’d like to adjust the Origin and Direction of my moving image w…

---

## [Progress reporting with strange behaviour](https://discourse.itk.org/t/progress-reporting-with-strange-behaviour/4398)

<div class="topic-metadata">

**Author:** [@Anders\_G](https://discourse.itk.org/u/Anders_G)\
**Replies:** 1\
**Last updated:** [September 8, 2021, 1:48pm UTC](https://discourse.itk.org/t/progress-reporting-with-strange-behaviour/4398 "2021-09-08T13:48:01Z")

</div>

Im quite new to simpleITK so this is perhaps simple. But I just don’t get it. When I look at the progress of a filter, (I register a Command so I can follow the progress) it behaves strangely. For most filters like the …

---

## [Pixel type error when using MergeLabelMapFilter](https://discourse.itk.org/t/pixel-type-error-when-using-mergelabelmapfilter/4390)

<div class="topic-metadata">

**Author:** [@mattwarkentin](https://discourse.itk.org/u/mattwarkentin)\
**Replies:** 5\
**Last updated:** [August 31, 2021, 7:52pm UTC](https://discourse.itk.org/t/pixel-type-error-when-using-mergelabelmapfilter/4390 "2021-08-31T19:52:39Z")

</div>

Hi, I am running into an error when trying to merge several label maps/masks into one label map. The basics of my code are: import SimpleITK as sitk map\_files = \['label\_map1.nrrd', 'label\_map2.nrrd'\] map\_imgs = \[sitk.…

---

## [What attributes to write from CompositeTransform Object to which DICOM tags?](https://discourse.itk.org/t/what-attributes-to-write-from-compositetransform-object-to-which-dicom-tags/4376)

<div class="topic-metadata">

**Author:** [@wafflesaregreat](https://discourse.itk.org/u/wafflesaregreat)\
**Replies:** 1\
**Last updated:** [August 29, 2021, 6:40pm UTC](https://discourse.itk.org/t/what-attributes-to-write-from-compositetransform-object-to-which-dicom-tags/4376 "2021-08-29T18:40:03Z")

</div>

Hi everyone, I’m just wondering what kind of information should be written to DICOM meta tags. Ideally, everything regarding the translation and rotation matrices should be written for Image Fusion/Registration purposes …

---

## [How to write unit testing in itk?](https://discourse.itk.org/t/how-to-write-unit-testing-in-itk/4371)

<div class="topic-metadata">

**Author:** [@priyanka](https://discourse.itk.org/u/priyanka)\
**Replies:** 1\
**Last updated:** [August 26, 2021, 7:46pm UTC](https://discourse.itk.org/t/how-to-write-unit-testing-in-itk/4371 "2021-08-26T19:46:04Z")

</div>

I found “ITKTestHarness” in itk testing framework but I’m getting errors while building it. I’m getting no idea how unit test for images in itk?

---

## [reading stack of images and writing as single image](https://discourse.itk.org/t/reading-stack-of-images-and-writing-as-single-image/4360)

<div class="topic-metadata">

**Author:** [@Won\_Chul\_Chung](https://discourse.itk.org/u/Won_Chul_Chung)\
**Replies:** 3\
**Last updated:** [August 26, 2021, 12:51pm UTC](https://discourse.itk.org/t/reading-stack-of-images-and-writing-as-single-image/4360 "2021-08-26T12:51:43Z")

</div>

Hello, I am trying to perform a simple task where I read in images with for loop, join them together and write it as a single image. But somehow sitk.JoinSeriesImageFilter does not join the images into a single stack, i…

---

## [Write German Umlauts into MetaData with SimpleITK](https://discourse.itk.org/t/write-german-umlauts-into-metadata-with-simpleitk/4355)

<div class="topic-metadata">

**Author:** [@Philip](https://discourse.itk.org/u/Philip)\
**Replies:** 5\
**Last updated:** [August 26, 2021, 7:09am UTC](https://discourse.itk.org/t/write-german-umlauts-into-metadata-with-simpleitk/4355 "2021-08-26T07:09:09Z")

</div>

Hello friends, I’ve got a problem I am not able to solve. I have to write a German word containing the letters ‘ö’ and ‘ä’ into the MetaData of our Dicom-File. However SITK’s SetMetaData refuses to write it. It always g…

---

## [SimpleElastix build issues](https://discourse.itk.org/t/simpleelastix-build-issues/4364)

<div class="topic-metadata">

**Author:** [@i.v.prgrmmr](https://discourse.itk.org/u/i.v.prgrmmr)\
**Replies:** 4\
**Last updated:** [August 25, 2021, 3:28pm UTC](https://discourse.itk.org/t/simpleelastix-build-issues/4364 "2021-08-25T15:28:29Z")

</div>

Hey @sag, Right now I am running into the same problem. However, I am a bit confused, what paths should I define for PYTHON \_EXECUTABLE PYTHON \_INCLUDE\_DIR PYTHON \_LIBRARY? I still have anaconda3. Thanks in advance!

---

## [includes target "gdcmjpeg8" more than once in the export set](https://discourse.itk.org/t/includes-target-gdcmjpeg8-more-than-once-in-the-export-set/4344)

<div class="topic-metadata">

**Author:** [@longjiang321](https://discourse.itk.org/u/longjiang321)\
**Replies:** 4\
**Last updated:** [August 19, 2021, 2:32pm UTC](https://discourse.itk.org/t/includes-target-gdcmjpeg8-more-than-once-in-the-export-set/4344 "2021-08-19T14:32:40Z")

</div>

hi friends: I am trying to compile the ITK source code with cmake, the version of ITK is 5.2.1. if I enable the option BUILD\_SHARED\_LIBS, the configure is successfully but generate failed. the error as below: , if…

---

## [Image with defective pixels while export in different image formats(.png, .tiff)](https://discourse.itk.org/t/image-with-defective-pixels-while-export-in-different-image-formats-png-tiff/4340)

<div class="topic-metadata">

**Author:** [@rubellion](https://discourse.itk.org/u/rubellion)\
**Replies:** 3\
**Last updated:** [August 19, 2021, 4:35am UTC](https://discourse.itk.org/t/image-with-defective-pixels-while-export-in-different-image-formats-png-tiff/4340 "2021-08-19T04:35:32Z")

</div>

Good day, while i try to export single image from .nii file in result i get an image but with defective pixels. I also tried to cast image from sitkUInt8 to sitkUInt16 but it become worse. import sys import SimpleITK as…

---

## [Unable to Reading pixel data from DICOM and store in an array.](https://discourse.itk.org/t/unable-to-reading-pixel-data-from-dicom-and-store-in-an-array/4293)

<div class="topic-metadata">

**Author:** [@priyanka](https://discourse.itk.org/u/priyanka)\
**Replies:** 2\
**Last updated:** [August 18, 2021, 7:49am UTC](https://discourse.itk.org/t/unable-to-reading-pixel-data-from-dicom-and-store-in-an-array/4293 "2021-08-18T07:49:48Z")

</div>

I tried printing with tags but I’m finding difficulty.

---

## [SimpleITK ImageFileWriter give a wrong tag](https://discourse.itk.org/t/simpleitk-imagefilewriter-give-a-wrong-tag/4334)

<div class="topic-metadata">

**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 2\
**Last updated:** [August 16, 2021, 2:48am UTC](https://discourse.itk.org/t/simpleitk-imagefilewriter-give-a-wrong-tag/4334 "2021-08-16T02:48:37Z")

</div>

I have some process for a image, and I want to save the result. The complete code to save image is: writer = sitk.ImageFileWriter() writer.KeepOriginalImageUIDOn() writer…

---

## [SimpleITK: demons registration filter requere the size of fixed/moving image to be the same](https://discourse.itk.org/t/simpleitk-demons-registration-filter-requere-the-size-of-fixed-moving-image-to-be-the-same/4335)

<div class="topic-metadata">

**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 1\
**Last updated:** [August 15, 2021, 3:29pm UTC](https://discourse.itk.org/t/simpleitk-demons-registration-filter-requere-the-size-of-fixed-moving-image-to-be-the-same/4335 "2021-08-15T15:29:31Z")

</div>

I want to use the demons registration method of SimpleITK between two images with different image size. For example, a 64X64X64 (moving image) and 128X128X128 (fixed image). import SimpleITK as sitk import numpy as np f…

---

## [Help getting started with python wrapping](https://discourse.itk.org/t/help-getting-started-with-python-wrapping/3612)

<div class="topic-metadata">

**Author:** [@doconnell](https://discourse.itk.org/u/doconnell)\
**Replies:** 9\
**Last updated:** [August 13, 2021, 8:47am UTC](https://discourse.itk.org/t/help-getting-started-with-python-wrapping/3612 "2021-08-13T08:47:48Z")

</div>

Hello, I’m having some trouble using the ITK python wrapping functionality. I’m trying to work through the basic python examples but I’m unable to import ITK even after copying the WrapITK.pth file to my site-packages d…

---

## [Splitting a 3D image into a 4D image then saving (C++)](https://discourse.itk.org/t/splitting-a-3d-image-into-a-4d-image-then-saving-c/4316)

<div class="topic-metadata">

**Author:** [@kevo](https://discourse.itk.org/u/kevo)\
**Replies:** 5\
**Last updated:** [August 11, 2021, 5:20pm UTC](https://discourse.itk.org/t/splitting-a-3d-image-into-a-4d-image-then-saving-c/4316 "2021-08-11T17:20:10Z")

</div>

Dear ITK community, I would like to take a 3D segmentation (nifti) and then create a new 4D nifti where the 4th dimension has has split up the label image where each element is the 3D image with just one label in each o…

---

## [SimpleTK installation on windows vs2019/vs2017](https://discourse.itk.org/t/simpletk-installation-on-windows-vs2019-vs2017/4314)

<div class="topic-metadata">

**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 1\
**Last updated:** [August 6, 2021, 12:24pm UTC](https://discourse.itk.org/t/simpletk-installation-on-windows-vs2019-vs2017/4314 "2021-08-06T12:24:05Z")

</div>

Hi all, I believe this is the worst happened to me trying to use SimpleITK suite open source. I am trying to use SimpleITK just like ITK and vtk with c++ on windows or Ubuntu machines. I firstly attempted on windows. So…

---

## [SimpleITK ScaleTransform understanding](https://discourse.itk.org/t/simpleitk-scaletransform-understanding/4313)

<div class="topic-metadata">

**Author:** [@Theoretialperson](https://discourse.itk.org/u/Theoretialperson)\
**Replies:** 2\
**Last updated:** [August 5, 2021, 7:37pm UTC](https://discourse.itk.org/t/simpleitk-scaletransform-understanding/4313 "2021-08-05T19:37:20Z")

</div>

I want to scale a 3D image by some factor, and I was expecting that the scale factor in ScaleTransform would give me a zoomed-out image when the scale factor is smaller than 1.0. Unfortunately this is not the case. I get…

---

## [3D niigz Affine Registration](https://discourse.itk.org/t/3d-niigz-affine-registration/4007)

<div class="topic-metadata">

**Author:** [@qxs](https://discourse.itk.org/u/qxs)\
**Replies:** 3\
**Last updated:** [August 5, 2021, 9:32am UTC](https://discourse.itk.org/t/3d-niigz-affine-registration/4007 "2021-08-05T09:32:33Z")

</div>

Hello All, I have some 3D CT brain images in nii.gz format. I would like to use one image as fixed image and another as moving image. I also have some blood vessels in vtk format in Image Coordinate System and in World…

---

## [Failed to compile ITKGrowCut](https://discourse.itk.org/t/failed-to-compile-itkgrowcut/4298)

<div class="topic-metadata">

**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 1\
**Last updated:** [August 2, 2021, 2:32pm UTC](https://discourse.itk.org/t/failed-to-compile-itkgrowcut/4298 "2021-08-02T14:32:08Z")

</div>

I want to use ITKGrowCut in my project, but I met some trouble to compile it. The code is download fro github. In the first time, I successfully compile it with Build\_Testing off. But, when I include the itkFastGrowCut.…

[Previous page](https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=18)

[Next page](https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=20)