# Beginner Questions

**URL:** https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=20

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

**Page:** 21

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## [Resampling .nii to isotropic spacing + fixed size](https://discourse.itk.org/t/resampling-nii-to-isotropic-spacing-fixed-size/4303)

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**Author:** [@Meliz](https://discourse.itk.org/u/Meliz)\
**Replies:** 3\
**Last updated:** [August 2, 2021, 1:33pm UTC](https://discourse.itk.org/t/resampling-nii-to-isotropic-spacing-fixed-size/4303 "2021-08-02T13:33:30Z")

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Hi, I am trying to resample a set of 3D volumes to train a Deep Learning network. I would like to resample them all to a specific size (say 64,64,64), but the catch is that for ease (not a necessity) of computing a loss…

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## [The surface created from Marching Cube and the mesh created from it is not smooth enough](https://discourse.itk.org/t/the-surface-created-from-marching-cube-and-the-mesh-created-from-it-is-not-smooth-enough/2444)

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**Author:** [@Sara\_Caffe](https://discourse.itk.org/u/Sara_Caffe)\
**Replies:** 8\
**Last updated:** [July 27, 2021, 8:28am UTC](https://discourse.itk.org/t/the-surface-created-from-marching-cube-and-the-mesh-created-from-it-is-not-smooth-enough/2444 "2021-07-27T08:28:26Z")

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Hi, I am still in the process of learning ITK/VTK and struggling for a few days to create a mesh with three types (triangle, tetrahedron, and Simplex) of cells from the binary mask volume. I feel that I am doing some m…

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## [ITK installation error](https://discourse.itk.org/t/itk-installation-error/3032)

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**Author:** [@Yolkandwhite](https://discourse.itk.org/u/Yolkandwhite)\
**Replies:** 8\
**Last updated:** [July 24, 2021, 9:02pm UTC](https://discourse.itk.org/t/itk-installation-error/3032 "2021-07-24T21:02:52Z")

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Hi I’m trying to build ITK. I’m using windows. I have downloaded the source code and configured and generate with cmake. next I opened ITK.sln with visual studio 2019 and start building ALL\_BUILD. after the build is …

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## [How to convert NIFTI or DICOM images into 3D mesh by using ITK?](https://discourse.itk.org/t/how-to-convert-nifti-or-dicom-images-into-3d-mesh-by-using-itk/4265)

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**Author:** [@Truring](https://discourse.itk.org/u/Truring)\
**Replies:** 5\
**Last updated:** [July 17, 2021, 11:34pm UTC](https://discourse.itk.org/t/how-to-convert-nifti-or-dicom-images-into-3d-mesh-by-using-itk/4265 "2021-07-17T23:34:07Z")

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I’m using ITK for spine reconstruction. I have some spine segmentation images in NIFTI format, how can I use ITK to reconstruct 3D spine mesh from these segmentation nifti images?

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## [Display 3D image using ITK and VTK](https://discourse.itk.org/t/display-3d-image-using-itk-and-vtk/897)

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**Author:** [@mabou](https://discourse.itk.org/u/mabou)\
**Replies:** 15\
**Last updated:** [August 4, 2020, 9:53am UTC](https://discourse.itk.org/t/display-3d-image-using-itk-and-vtk/897 "2020-08-04T09:53:29Z")

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Hi, I am using simple code which I found in ITK Example. I need to display nifti image, but all I got is black box. And when I hover the mouse over the window, the color changes from black to white, and I can’t see the…

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## [rotational MIP around a specified axis in physical coordinates system](https://discourse.itk.org/t/rotational-mip-around-a-specified-axis-in-physical-coordinates-system/4255)

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**Author:** [@Stephan\_Hahn1](https://discourse.itk.org/u/Stephan_Hahn1)\
**Replies:** 3\
**Last updated:** [July 13, 2021, 12:49pm UTC](https://discourse.itk.org/t/rotational-mip-around-a-specified-axis-in-physical-coordinates-system/4255 "2021-07-13T12:49:55Z")

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Hi everyone. I have a very simple question that maybe @zivy can answer (based on previous related topics). I want to generate a rotational MIP around a specified axis with an image that has not an unit direction cosine…

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## [SimpleITK installation in linux docker container](https://discourse.itk.org/t/simpleitk-installation-in-linux-docker-container/4241)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 0\
**Last updated:** [July 2, 2021, 10:22pm UTC](https://discourse.itk.org/t/simpleitk-installation-in-linux-docker-container/4241 "2021-07-02T22:22:42Z")

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Hi All, I am glad to announce that I could finally build simpleitk as an docker image using Dockerfile provided by ITK group forum and I thank all of you. The problem with my hardware caused SuperBuild to fail inside t…

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## [writing mhd + raw instead of mhd +zraw](https://discourse.itk.org/t/writing-mhd-raw-instead-of-mhd-zraw/4109)

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**Author:** [@totoro3y](https://discourse.itk.org/u/totoro3y)\
**Replies:** 4\
**Last updated:** [June 30, 2021, 12:49pm UTC](https://discourse.itk.org/t/writing-mhd-raw-instead-of-mhd-zraw/4109 "2021-06-30T12:49:55Z")

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Hello, I am using simpleitk to write mhd files using sitk.WriteImage(img, ‘file.mhd’) The output file is of mhd + zraw type. How can I generate mhd + raw files using simpleitk? Thank you in advance!

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## [Get Patient Orientation and convert to OpenGL Coordinates](https://discourse.itk.org/t/get-patient-orientation-and-convert-to-opengl-coordinates/4219)

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**Author:** [@saravanan](https://discourse.itk.org/u/saravanan)\
**Replies:** 1\
**Last updated:** [June 18, 2021, 12:34pm UTC](https://discourse.itk.org/t/get-patient-orientation-and-convert-to-opengl-coordinates/4219 "2021-06-18T12:34:59Z")

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I am using itk::ImageSeriesReader to read the DICOM image set. I need the patient orientation information / matrix for use in my OpenGL program. Thanks

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## [use ITK on the web](https://discourse.itk.org/t/use-itk-on-the-web/4183)

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**Author:** [@zrxiaojie](https://discourse.itk.org/u/zrxiaojie)\
**Replies:** 9\
**Last updated:** [June 15, 2021, 2:46pm UTC](https://discourse.itk.org/t/use-itk-on-the-web/4183 "2021-06-15T14:46:30Z")

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Hi, I’m new to ITK and interested in medical image processing on the web. I tried using itk-js (insightsoftwareconsortium.github.io) to read a dicom series, then showed them on the web through vtk.js. It worked. However,…

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## [Stopping optimization by metric value for demons filters](https://discourse.itk.org/t/stopping-optimization-by-metric-value-for-demons-filters/4190)

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**Author:** [@bbikdash](https://discourse.itk.org/u/bbikdash)\
**Replies:** 6\
**Last updated:** [June 15, 2021, 12:46pm UTC](https://discourse.itk.org/t/stopping-optimization-by-metric-value-for-demons-filters/4190 "2021-06-15T12:46:27Z")

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Hi, I’m currently using the Python demons registration filters (DemonsRegistrationFilter, DifferomorphicDRF, SymmetricDRF, etc.) from SimpleITK to perform non-rigid image registration on x-rays for my research. Is ther…

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## [make ../SimpleITK/SuperBuild inside ubuntu container error](https://discourse.itk.org/t/make-simpleitk-superbuild-inside-ubuntu-container-error/4177)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 19\
**Last updated:** [June 14, 2021, 12:25pm UTC](https://discourse.itk.org/t/make-simpleitk-superbuild-inside-ubuntu-container-error/4177 "2021-06-14T12:25:29Z")

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Dear All, I AM SORRY TO POST THE Dockerfile in such messy way, but i have a problem with building the SimpleITK from within the ubuntu container prepared specifically for SimpleITK image for running a container that has…

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## [SimpleITK build in windows 10](https://discourse.itk.org/t/simpleitk-build-in-windows-10/4205)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 1\
**Last updated:** [June 14, 2021, 12:18pm UTC](https://discourse.itk.org/t/simpleitk-build-in-windows-10/4205 "2021-06-14T12:18:49Z")

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Hi All, I am stuck in the build and installation of simpleitk inside a docker container Linux. I am trying to figure out couple of things, so I decided to install the simpleitk in the windows hopefully the latest versi…

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## [Reading a .Nrrd file having 3 dimenisions (X,Y,numSlice) and visualizing them in a sequence.](https://discourse.itk.org/t/reading-a-nrrd-file-having-3-dimenisions-x-y-numslice-and-visualizing-them-in-a-sequence/4179)

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**Author:** [@srivastava.va](https://discourse.itk.org/u/srivastava.va)\
**Replies:** 5\
**Last updated:** [June 10, 2021, 5:20pm UTC](https://discourse.itk.org/t/reading-a-nrrd-file-having-3-dimenisions-x-y-numslice-and-visualizing-them-in-a-sequence/4179 "2021-06-10T17:20:27Z")

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Hello, I am just beginning to write code using ITK and have been wondering how to read .Nrrd files. So far I have written this code : I am not sure how to visualize the 2D slice data that I have stored in the img. I…

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## [NiftiImageIO class in python simpleitk ?](https://discourse.itk.org/t/niftiimageio-class-in-python-simpleitk/4201)

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**Author:** [@cbhushan](https://discourse.itk.org/u/cbhushan)\
**Replies:** 1\
**Last updated:** [June 10, 2021, 5:53pm UTC](https://discourse.itk.org/t/niftiimageio-class-in-python-simpleitk/4201 "2021-06-10T17:53:32Z")

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I am trying to write a nifti file with custom RescaleSlope, RescaleIntercept and was hoping to use NiftiImageIO’s SetRescaleSlope() and SetRescaleIntercept(). Is it possible to access functionality of NiftiImageIO class …

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## [How to apply transform to strictly a subset of an image?](https://discourse.itk.org/t/how-to-apply-transform-to-strictly-a-subset-of-an-image/4195)

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**Author:** [@jingxuan](https://discourse.itk.org/u/jingxuan)\
**Replies:** 1\
**Last updated:** [June 10, 2021, 1:19pm UTC](https://discourse.itk.org/t/how-to-apply-transform-to-strictly-a-subset-of-an-image/4195 "2021-06-10T13:19:29Z")

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Hello. I have some conceptual understanding of registration and very little of its math so I’m looking for a practical solution. Thank you in advance for any help offered. Say I registered 3D image A to 3D image B in a …

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## [Add ITK in Qt](https://discourse.itk.org/t/add-itk-in-qt/4188)

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**Author:** [@Roberto722](https://discourse.itk.org/u/Roberto722)\
**Replies:** 2\
**Last updated:** [June 9, 2021, 6:32pm UTC](https://discourse.itk.org/t/add-itk-in-qt/4188 "2021-06-09T18:32:41Z")

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Hello, i am noob in linking libraries with Qt. I would like to know if someone has a comprehensive guide on how to add and make ITK libraries working in Qt and then write some easy lines of code to see that working.

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## [Linking Fiji with ITK](https://discourse.itk.org/t/linking-fiji-with-itk/4186)

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**Author:** [@alrojo](https://discourse.itk.org/u/alrojo)\
**Replies:** 2\
**Last updated:** [June 8, 2021, 4:44am UTC](https://discourse.itk.org/t/linking-fiji-with-itk/4186 "2021-06-08T04:44:43Z")

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In TUTORIAL/00\_setup.ipynb I cannot seem to make SimpleITK use my Fiji.app or ImageJ installation For the following code snippet: # Retrieve an image from the network, read it and display using the external viewer imag…

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## [ninja build for simpleitk is stuck](https://discourse.itk.org/t/ninja-build-for-simpleitk-is-stuck/4184)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 0\
**Last updated:** [June 6, 2021, 5:29pm UTC](https://discourse.itk.org/t/ninja-build-for-simpleitk-is-stuck/4184 "2021-06-06T17:29:18Z")

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Hi All, SimpleITK build.ninja for VM docker container linux is stuck after downloading external data SHA512/…stuck at \[898/3100\]building CXX Object code/BasicFilters/src/CMakeFiles/SimpleITK\_ITKImageGrid.dir/sitkTileIma…

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## [SimpleITK installation in linux container](https://discourse.itk.org/t/simpleitk-installation-in-linux-container/4180)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 0\
**Last updated:** [June 4, 2021, 4:14pm UTC](https://discourse.itk.org/t/simpleitk-installation-in-linux-container/4180 "2021-06-04T16:14:39Z")

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Hi All, I have tried to follow the getting started with SimpleITK in linux, I have now two folder SimpleITK, SimpleITK-build, I did run cmake …/SimpleITK/Superbuild/ from inside the SimpleITK-build, it is successfully d…

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## [Using SCIFIO for reading Whole Slide Images at different resolutions.](https://discourse.itk.org/t/using-scifio-for-reading-whole-slide-images-at-different-resolutions/4171)

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**Author:** [@Jason\_Daniel](https://discourse.itk.org/u/Jason_Daniel)\
**Replies:** 2\
**Last updated:** [June 2, 2021, 2:19pm UTC](https://discourse.itk.org/t/using-scifio-for-reading-whole-slide-images-at-different-resolutions/4171 "2021-06-02T14:19:09Z")

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Hi Everyone, I’m new to ITK and I am using SCIFIO to read in whole slide images from proprietary image formats: “.svs .vms .bif” etc. I want to know if it is possible to read the image in at a different resolution direct…

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## [sitk.Resample returns empty image](https://discourse.itk.org/t/sitk-resample-returns-empty-image/4169)

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**Author:** [@emirhan](https://discourse.itk.org/u/emirhan)\
**Replies:** 1\
**Last updated:** [June 2, 2021, 3:01pm UTC](https://discourse.itk.org/t/sitk-resample-returns-empty-image/4169 "2021-06-02T15:01:25Z")

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I am trying to implement an atlas based segmentation model; however, when I resample after registration, I always get an image full of zeros. Registration function (input images are non empty images of size 240,240,155 …

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## [How can I catch the registered slices in 'moving\_resampled' and save them in a folder?](https://discourse.itk.org/t/how-can-i-catch-the-registered-slices-in-moving-resampled-and-save-them-in-a-folder/4170)

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**Author:** [@Aya\_Hassan](https://discourse.itk.org/u/Aya_Hassan)\
**Replies:** 2\
**Last updated:** [May 31, 2021, 2:56pm UTC](https://discourse.itk.org/t/how-can-i-catch-the-registered-slices-in-moving-resampled-and-save-them-in-a-folder/4170 "2021-05-31T14:56:18Z")

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Hello Everyone, I have done registration between MRI and CT scans, and I wanna save the output of registered slices? import matplotlib.pyplot as plt import SimpleITK as sitk from ipywidgets import interact, fixed from …

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## [RuntimeError: No suitable template parameter can be found](https://discourse.itk.org/t/runtimeerror-no-suitable-template-parameter-can-be-found/4159)

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**Author:** [@nbob](https://discourse.itk.org/u/nbob)\
**Replies:** 14\
**Last updated:** [May 28, 2021, 1:32pm UTC](https://discourse.itk.org/t/runtimeerror-no-suitable-template-parameter-can-be-found/4159 "2021-05-28T13:32:43Z")

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Hello, I am trying to replicate the code from this notebook ITK-Watershed to Label Bubbles | Kaggle for 3D watershed segmentation locally. It runs in the notebook, however, locally, itk.GetArrayFromImage(watershedOp) yi…

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## [Isotropic resampling of a CT scan](https://discourse.itk.org/t/isotropic-resampling-of-a-ct-scan/4160)

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**Author:** [@mattwarkentin](https://discourse.itk.org/u/mattwarkentin)\
**Replies:** 10\
**Last updated:** [May 27, 2021, 6:02pm UTC](https://discourse.itk.org/t/isotropic-resampling-of-a-ct-scan/4160 "2021-05-27T18:02:02Z")

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Hi, I am working on resampling and interpolating some CT scans to have isotropic voxel spacing (\[1, 1, 1\]). I have tried two approaches that both execute without error, but I am not sure why the first approach looks odd…

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## [ITKMontage double-conversion problem](https://discourse.itk.org/t/itkmontage-double-conversion-problem/4155)

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**Author:** [@lambdamoses](https://discourse.itk.org/u/lambdamoses)\
**Replies:** 1\
**Last updated:** [May 25, 2021, 10:53pm UTC](https://discourse.itk.org/t/itkmontage-double-conversion-problem/4155 "2021-05-25T22:53:54Z")

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I built ITK 5.2, pulled from GitHub, and built ITKMontage and the examples. It did build successfully. Then I tried to run ITKMontage’s example CompleteMontage. The ITKMontage examples come with a CMakeLists.txt. When I …

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## [Getting HU values after loading volume](https://discourse.itk.org/t/getting-hu-values-after-loading-volume/4142)

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**Author:** [@anillspawar](https://discourse.itk.org/u/anillspawar)\
**Replies:** 2\
**Last updated:** [May 20, 2021, 5:40pm UTC](https://discourse.itk.org/t/getting-hu-values-after-loading-volume/4142 "2021-05-20T17:40:49Z")

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Do we need to convert pixel values to HU values after reading CT volumes using simpleITK. Code I am using for reading volume: reader = SimpleITK.ImageSeriesReader() filenamesDICOM = reader.GetGDCMSeriesFileNames(pathD…

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## [Systematic kernel crash when using interpolator.Evaluate inside loop (python)](https://discourse.itk.org/t/systematic-kernel-crash-when-using-interpolator-evaluate-inside-loop-python/4121)

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**Author:** [@Benjamin-Fouquet](https://discourse.itk.org/u/Benjamin-Fouquet)\
**Replies:** 3\
**Last updated:** [May 19, 2021, 5:44pm UTC](https://discourse.itk.org/t/systematic-kernel-crash-when-using-interpolator-evaluate-inside-loop-python/4121 "2021-05-19T17:44:38Z")

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Hello there, I just started to fiddle with itk at the lab. What I was trying to do is to fetch the texture of a nifti image and plug it to a corresponding mesh, interpolating a pixel intensity value as needed. Code look…

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## [Image format for exercise 1.7 Extracting Slices](https://discourse.itk.org/t/image-format-for-exercise-1-7-extracting-slices/4085)

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**Author:** [@rohit\_inippully](https://discourse.itk.org/u/rohit_inippully)\
**Replies:** 3\
**Last updated:** [May 14, 2021, 2:28pm UTC](https://discourse.itk.org/t/image-format-for-exercise-1-7-extracting-slices/4085 "2021-05-14T14:28:56Z")

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Hi, I am going through the guide for ITK. I am not sure which image file format I need to use for exercise 1.7 to extract a slice. Could anyone please advise? thank you.

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## [SimpleITK on Android](https://discourse.itk.org/t/simpleitk-on-android/4126)

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**Author:** [@hina-shah](https://discourse.itk.org/u/hina-shah)\
**Replies:** 1\
**Last updated:** [May 13, 2021, 1:02pm UTC](https://discourse.itk.org/t/simpleitk-on-android/4126 "2021-05-13T13:02:13Z")

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Hi All, We are looking into building a small app that reads ultrasound cines (basically dicom files) and processes them on mobile devices. It looks like SimpleITK has Java support, but I was wondering if there are any o…

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