# Beginner Questions **URL:** https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=16 [Latest](https://discourse.itk.org/latest.md) · [Categories](https://discourse.itk.org/categories.md) · [Tags](https://discourse.itk.org/tags.md) **Page:** 17 --- ## [How to convert 3D rgb to grascale](https://discourse.itk.org/t/how-to-convert-3d-rgb-to-grascale/4908)
**Author:** [@assia855](https://discourse.itk.org/u/assia855)\ **Replies:** 7\ **Last updated:** [April 19, 2022, 10:38am UTC](https://discourse.itk.org/t/how-to-convert-3d-rgb-to-grascale/4908 "2022-04-19T10:38:07Z")
Hello Folks, I’m searching for how to convert my 3D data to grayscale. I can’t find how on the documentation. Thanks in advance. --- ## [Extracting displacement fields from rigid registration](https://discourse.itk.org/t/extracting-displacement-fields-from-rigid-registration/4834)
**Author:** [@edgar](https://discourse.itk.org/u/edgar)\ **Replies:** 16\ **Last updated:** [April 14, 2022, 9:20am UTC](https://discourse.itk.org/t/extracting-displacement-fields-from-rigid-registration/4834 "2022-04-14T09:20:57Z")
Hello! Continuing the discussion from 3D image registration with Python and without SimpleITK: Once I have a registration, what is the best way to extract the deformation field (a.k.a. displacement field) with ITK Py… --- ## [ITK not working in Python](https://discourse.itk.org/t/itk-not-working-in-python/4733)
**Author:** [@ogdenk](https://discourse.itk.org/u/ogdenk)\ **Replies:** 22\ **Last updated:** [April 13, 2022, 1:42pm UTC](https://discourse.itk.org/t/itk-not-working-in-python/4733 "2022-04-13T13:42:06Z")
Hi all, I have a very basic question. I am learning to use ITK in Python, and I can’t seem to get it to work. In a simple example, I am just trying to use a median image filter, but copying online examples doesn’t work… --- ## [How to normalize a 3D volume](https://discourse.itk.org/t/how-to-normalize-a-3d-volume/4906)
**Author:** [@assia855](https://discourse.itk.org/u/assia855)\ **Replies:** 6\ **Last updated:** [April 7, 2022, 3:30pm UTC](https://discourse.itk.org/t/how-to-normalize-a-3d-volume/4906 "2022-04-07T15:30:32Z")
Hello folks, I would like to normalize a 3D volume but I can’t find a ressource. Please can you suggest to me a code or library, I would be grateful. Thanks in advance. --- ## [Multiresolution Registration with 2D Affine Transformation on pairs of 2D images](https://discourse.itk.org/t/multiresolution-registration-with-2d-affine-transformation-on-pairs-of-2d-images/3096)
**Author:** [@ScottP](https://discourse.itk.org/u/ScottP)\ **Replies:** 20\ **Last updated:** [April 3, 2022, 7:21pm UTC](https://discourse.itk.org/t/multiresolution-registration-with-2d-affine-transformation-on-pairs-of-2d-images/3096 "2022-04-03T19:21:15Z")
Hello, I’m a beginner to registration (1 month experience) and semi-beginner to Python (4 months). I need to do multiresolution registration in Python with 2D Affine transformation on pairs of 2D fixed and 2D moving ima… --- ## [Apply 2D Affine transformation to a 3D image](https://discourse.itk.org/t/apply-2d-affine-transformation-to-a-3d-image/4899)
**Author:** [@Moha\_data](https://discourse.itk.org/u/Moha_data)\ **Replies:** 3\ **Last updated:** [April 1, 2022, 7:05pm UTC](https://discourse.itk.org/t/apply-2d-affine-transformation-to-a-3d-image/4899 "2022-04-01T19:05:09Z")
Hello, How can I apply the result of 2D affine registration to a 3D image? For now, I just consider a 3D image as a series of 2D images and apply the transformation to each of them, which is not efficient. I appreciate … --- ## [what is the difference between using DCMTKImageIO and GDCMImageIO ?](https://discourse.itk.org/t/what-is-the-difference-between-using-dcmtkimageio-and-gdcmimageio/4897)
**Author:** [@mmeltsner](https://discourse.itk.org/u/mmeltsner)\ **Replies:** 1\ **Last updated:** [April 1, 2022, 1:23pm UTC](https://discourse.itk.org/t/what-is-the-difference-between-using-dcmtkimageio-and-gdcmimageio/4897 "2022-04-01T13:23:39Z")
I have been using generally GDCMImageIO for the ImageFileReader for reading dicom files from disk, but I recently discovered another ImageIO called DCMTKImageIO which seems to use the dcmtk toolkit instead of the gdcm to… --- ## [itk::LabelGeometryImageFilter GetMajorAxisLength() return type](https://discourse.itk.org/t/itk-labelgeometryimagefilter-getmajoraxislength-return-type/4876)
**Author:** [@anillspawar](https://discourse.itk.org/u/anillspawar)\ **Replies:** 4\ **Last updated:** [March 26, 2022, 8:51pm UTC](https://discourse.itk.org/t/itk-labelgeometryimagefilter-getmajoraxislength-return-type/4876 "2022-03-26T20:51:48Z")
I am using itk::LabelGeometryImageFilter to GetMajorAxisLength() of an object. I want to know the return unit of length given, is it in millimeter or pixel? If it is in pixel how to convert it into millimeter? Thanks i… --- ## [Centerline extraction](https://discourse.itk.org/t/centerline-extraction/4885)
**Author:** [@ekmungi](https://discourse.itk.org/u/ekmungi)\ **Replies:** 7\ **Last updated:** [March 25, 2022, 5:46pm UTC](https://discourse.itk.org/t/centerline-extraction/4885 "2022-03-25T17:46:42Z")
I am new to ITK. I have a 3D model of a tubular structure and I am looking for a way to extract the centerline for it. Could someone help? So far, I have tried using VMTK but it requires a closed model (end points are c… --- ## [itk.js readImageDICOMFileSeries](https://discourse.itk.org/t/itk-js-readimagedicomfileseries/2086)
**Author:** [@aliu4](https://discourse.itk.org/u/aliu4)\ **Replies:** 2\ **Last updated:** [March 24, 2022, 4:12pm UTC](https://discourse.itk.org/t/itk-js-readimagedicomfileseries/2086 "2022-03-24T16:12:08Z")
hello, I am developing an application in vue-js and im having issues with the readImageDICOMFileSeries method. I’m currently not using a web-worker and it keeps returning this error. “ImageIO.worker.js:1 Uncaught Syntax… --- ## [Read, manipulate tags and write dicom series](https://discourse.itk.org/t/read-manipulate-tags-and-write-dicom-series/4863)
**Author:** [@csad6517](https://discourse.itk.org/u/csad6517)\ **Replies:** 6\ **Last updated:** [March 24, 2022, 12:29pm UTC](https://discourse.itk.org/t/read-manipulate-tags-and-write-dicom-series/4863 "2022-03-24T12:29:26Z")
I am reading dicom series and manipulate some tags from it. Finally write the new series. I can change any dicom tag without any problems. They are correcly changed. But the new dataset is visualized wrongly. The axial s… --- ## [Inverting Resample Filter Execute operation](https://discourse.itk.org/t/inverting-resample-filter-execute-operation/4856)
**Author:** [@BraveDistribution](https://discourse.itk.org/u/BraveDistribution)\ **Replies:** 16\ **Last updated:** [March 16, 2022, 7:28pm UTC](https://discourse.itk.org/t/inverting-resample-filter-execute-operation/4856 "2022-03-16T19:28:10Z")
Hello, The problem that I am trying to solve with SimpleITK: 1/ I have a temporal sequence of volumes from the same patient 2/ I have one segmentation mask of the organ under observation. 3/ I want to get segmentatio… --- ## [Select output directory for series without namesgenerator](https://discourse.itk.org/t/select-output-directory-for-series-without-namesgenerator/4864)
**Author:** [@Oddone-Scatena](https://discourse.itk.org/u/Oddone-Scatena)\ **Replies:** 1\ **Last updated:** [March 15, 2022, 5:19pm UTC](https://discourse.itk.org/t/select-output-directory-for-series-without-namesgenerator/4864 "2022-03-15T17:19:30Z")
How to chose the output directory to save the files from dicom series writer (2D) if I am reading from a volume 3D?I am not using not using namesgenerator but numericseriesfilenames to generate the file names for my ser… --- ## [Read DICOM-RT to obtain structure volumes as arrays](https://discourse.itk.org/t/read-dicom-rt-to-obtain-structure-volumes-as-arrays/4860)
**Author:** [@RT\_newbie](https://discourse.itk.org/u/RT_newbie)\ **Replies:** 1\ **Last updated:** [March 13, 2022, 1:23pm UTC](https://discourse.itk.org/t/read-dicom-rt-to-obtain-structure-volumes-as-arrays/4860 "2022-03-13T13:23:30Z")
Hi all, What I want to do is overwriting HU value of a contoured structure in a CT image. Starting point is a CT image as DICOM sequence and a DICOM RT file for the structure set. I know how to read in the CT image an… --- ## [Deform CT image (DICOM) with DVF (mhd)](https://discourse.itk.org/t/deform-ct-image-dicom-with-dvf-mhd/4850)
**Author:** [@RT\_newbie](https://discourse.itk.org/u/RT_newbie)\ **Replies:** 4\ **Last updated:** [March 13, 2022, 7:01am UTC](https://discourse.itk.org/t/deform-ct-image-dicom-with-dvf-mhd/4850 "2022-03-13T07:01:13Z")
Hi :slight\_smile: I have a CT image as DICOM file and a deformation vector field as an .mhd file, which I want to use to deform the CT. The deformation vector field is a result from a deformable registration of the CT & … --- ## [Problem when opening a big TIF file](https://discourse.itk.org/t/problem-when-opening-a-big-tif-file/4858)
**Author:** [@Jeremie](https://discourse.itk.org/u/Jeremie)\ **Replies:** 0\ **Last updated:** [March 11, 2022, 11:38am UTC](https://discourse.itk.org/t/problem-when-opening-a-big-tif-file/4858 "2022-03-11T11:38:48Z")
Hello, I am doing mouse brains alignement to the Allen Brain Atlas. Samples are optically cleared and images are obtained on a light sheet microscope. I use ITK Elastix for registration. It works nicely on small files … --- ## [correction of gantry tilted ct image](https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841)
**Author:** [@csad6517](https://discourse.itk.org/u/csad6517)\ **Replies:** 16\ **Last updated:** [March 9, 2022, 4:38pm UTC](https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841 "2022-03-09T16:38:30Z")
Hello, I need help by understanding the correct pipleline and determining the share factor of a gantry tilted ct dataset, so that I can apply a transform on it. I know the exact angle of the gantry over read out DICOM … --- ## [Compilation of ITK from source with Python wrappers in Arch-based systems](https://discourse.itk.org/t/compilation-of-itk-from-source-with-python-wrappers-in-arch-based-systems/4843)
**Author:** [@edgar](https://discourse.itk.org/u/edgar)\ **Replies:** 10\ **Last updated:** [March 9, 2022, 3:03pm UTC](https://discourse.itk.org/t/compilation-of-itk-from-source-with-python-wrappers-in-arch-based-systems/4843 "2022-03-09T15:03:05Z")
Compilation of ITK from source with Python wrappers in Arch-based systems Continuing the discussion from Extracting displacement fields from rigid registration: Hello! I am having long days trying to correctly compil… --- ## [RegionOfInterestImageFilter to extract image slice from volume](https://discourse.itk.org/t/regionofinterestimagefilter-to-extract-image-slice-from-volume/4787)
**Author:** [@SofiaCV](https://discourse.itk.org/u/SofiaCV)\ **Replies:** 13\ **Last updated:** [February 28, 2022, 10:34am UTC](https://discourse.itk.org/t/regionofinterestimagefilter-to-extract-image-slice-from-volume/4787 "2022-02-28T10:34:20Z")
Hello, I’d like to extract a 2D slice from a MRI NIfTI file. I believe the RegionOfInterestImageFilter function in itk will do the job: https://itk.org/ITKExamples/src/Filtering/ImageGrid/ExtractRegionOfInterestInOneIm… --- ## [Is there any difference in performance (in Registration) between python and CSharp in SimpleITK?](https://discourse.itk.org/t/is-there-any-difference-in-performance-in-registration-between-python-and-csharp-in-simpleitk/4831)
**Author:** [@jpad](https://discourse.itk.org/u/jpad)\ **Replies:** 1\ **Last updated:** [February 27, 2022, 8:16pm UTC](https://discourse.itk.org/t/is-there-any-difference-in-performance-in-registration-between-python-and-csharp-in-simpleitk/4831 "2022-02-27T20:16:45Z")
I use version 2.2 of simpleitk. It was implemented by referring to the following code for registration. https://simpleitk.readthedocs.io/en/master/link\_ImageRegistrationMethodBSpline2\_docs.html Previously, image regis… --- ## [how to balance the illumination( Correction of Intensity Inhomogeneity) in itk Montage](https://discourse.itk.org/t/how-to-balance-the-illumination-correction-of-intensity-inhomogeneity-in-itk-montage/4811)
**Author:** [@allen](https://discourse.itk.org/u/allen)\ **Replies:** 17\ **Last updated:** [February 25, 2022, 2:27pm UTC](https://discourse.itk.org/t/how-to-balance-the-illumination-correction-of-intensity-inhomogeneity-in-itk-montage/4811 "2022-02-25T14:27:00Z")
hello, i use itk stitch microscope tiles to whole slide image, it works really good, yet there are some grid shadow in the blending area like this i looked into it, it’s caused by the uneven illumination, this article … --- ## [ITK Install issues on VS2022](https://discourse.itk.org/t/itk-install-issues-on-vs2022/4821)
**Author:** [@xyz](https://discourse.itk.org/u/xyz)\ **Replies:** 13\ **Last updated:** [February 24, 2022, 9:43am UTC](https://discourse.itk.org/t/itk-install-issues-on-vs2022/4821 "2022-02-24T09:43:28Z")
Dear all, I was trying to install ITK for transforming the .TRE files from ITKTubeTK - Bullitt - Healthy MR Database to common image format for phantom for several days. My environment is python 3.10, ITK 5.2.1/ITK 5.3r… --- ## [Odd behavior with Numpy Array Views](https://discourse.itk.org/t/odd-behavior-with-numpy-array-views/4827)
**Author:** [@brandonfosso](https://discourse.itk.org/u/brandonfosso)\ **Replies:** 2\ **Last updated:** [February 23, 2022, 1:31am UTC](https://discourse.itk.org/t/odd-behavior-with-numpy-array-views/4827 "2022-02-23T01:31:21Z")
Hello, I was just experimenting with SimpleITK in a Jupyter Notebook and was surprised by the following behavior. \> junk = np.zeros((3,3), dtype=np.uint8) \> junk array(\[\[0, 0, 0\], \[0, 0, 0\], \[0, 0, 0\]\], dt… --- ## [ImageSeriesReader read DICOM series with wrong order](https://discourse.itk.org/t/imageseriesreader-read-dicom-series-with-wrong-order/4813)
**Author:** [@hubutui](https://discourse.itk.org/u/hubutui)\ **Replies:** 7\ **Last updated:** [February 19, 2022, 2:05am UTC](https://discourse.itk.org/t/imageseriesreader-read-dicom-series-with-wrong-order/4813 "2022-02-19T02:05:09Z")
I read DICOM series according to this guide import SimpleITK as sitk reader = sitk.ImageSeriesReader() reader.SetFileNames(reader.GetGDCMSeriesFileNames("patient01")) img2 = reader.Execute() data2 = sitk.GetArrayFromIma… --- ## [Registration with a Versor with Python and without SimpleITK](https://discourse.itk.org/t/registration-with-a-versor-with-python-and-without-simpleitk/4806)
**Author:** [@edgar](https://discourse.itk.org/u/edgar)\ **Replies:** 12\ **Last updated:** [February 18, 2022, 2:07am UTC](https://discourse.itk.org/t/registration-with-a-versor-with-python-and-without-simpleitk/4806 "2022-02-18T02:07:56Z")
Continuing the discussion from 3D image registration with Python and without SimpleITK: Hello! Instead of the translation registration, I am now trying a registration with a versor. How can I do that? This is my code (… --- ## [how to use image streaming to reduce memory usage and cpu usage in image stitching](https://discourse.itk.org/t/how-to-use-image-streaming-to-reduce-memory-usage-and-cpu-usage-in-image-stitching/4795)
**Author:** [@allen](https://discourse.itk.org/u/allen)\ **Replies:** 10\ **Last updated:** [February 17, 2022, 2:52pm UTC](https://discourse.itk.org/t/how-to-use-image-streaming-to-reduce-memory-usage-and-cpu-usage-in-image-stitching/4795 "2022-02-17T14:52:15Z")
The cpu usage and memory usage is pretty high when stitching tiles into a single one. 140 tiles(2592\*1944) stitching occupy nearly 100% cpu usage for more than 60s. i wonder if the usage won’t be so high in the image st… --- ## [How to render DSA type DICOM file using JavaScript](https://discourse.itk.org/t/how-to-render-dsa-type-dicom-file-using-javascript/4809)
**Author:** [@sujaly](https://discourse.itk.org/u/sujaly)\ **Replies:** 3\ **Last updated:** [February 17, 2022, 4:20am UTC](https://discourse.itk.org/t/how-to-render-dsa-type-dicom-file-using-javascript/4809 "2022-02-17T04:20:53Z")
This file is of type DICOM, How to use JavaScript to play this file, --- ## [read Nifti and create transform](https://discourse.itk.org/t/read-nifti-and-create-transform/4785)
**Author:** [@jeffppp](https://discourse.itk.org/u/jeffppp)\ **Replies:** 8\ **Last updated:** [February 9, 2022, 3:11am UTC](https://discourse.itk.org/t/read-nifti-and-create-transform/4785 "2022-02-09T03:11:41Z")
Hello, I have a nii file. I can use SimpleITK to read it in c#. But it’s didn’t combine the transform information. It’s seems display the original image. I think maybe I should use the “Resample” to do this. But I d… --- ## [Difference between two lines in the documentation](https://discourse.itk.org/t/difference-between-two-lines-in-the-documentation/4782)
**Author:** [@edgar](https://discourse.itk.org/u/edgar)\ **Replies:** 2\ **Last updated:** [February 3, 2022, 2:46pm UTC](https://discourse.itk.org/t/difference-between-two-lines-in-the-documentation/4782 "2022-02-03T14:46:19Z")
Besides the comment lines, can someone tell me what is the difference between these 2? Thanks. # Here we specify the filter input explicitly median = itk.MedianImageFilter.New(reader.GetOutput()) # Same as above but sho… --- ## [Read Numpy array as itk.itkImagePython.itkImageF3](https://discourse.itk.org/t/read-numpy-array-as-itk-itkimagepython-itkimagef3/4776)
**Author:** [@edgar](https://discourse.itk.org/u/edgar)\ **Replies:** 11\ **Last updated:** [February 2, 2022, 11:12pm UTC](https://discourse.itk.org/t/read-numpy-array-as-itk-itkimagepython-itkimagef3/4776 "2022-02-02T23:12:56Z")
I just want to be able to use a numpy array as itk.itkImagePython.itkImageF3 to feed it into a registration (without SimpleITK). Thanks! Description of the issue with MWE I get an error when trying to run any of these i… [Previous page](https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=15) [Next page](https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=17)