# Beginner Questions **URL:** https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=1 [Latest](https://discourse.itk.org/latest.md) · [Categories](https://discourse.itk.org/categories.md) · [Tags](https://discourse.itk.org/tags.md) **Page:** 2 --- ## [Helper Function itk.tile\_image\_filter Correct Usage to Convert a 2D Slice to 3D Image](https://discourse.itk.org/t/helper-function-itk-tile-image-filter-correct-usage-to-convert-a-2d-slice-to-3d-image/7586)
**Author:** [@constantine](https://discourse.itk.org/u/constantine)\ **Replies:** 2\ **Last updated:** [June 30, 2025, 3:25pm UTC](https://discourse.itk.org/t/helper-function-itk-tile-image-filter-correct-usage-to-convert-a-2d-slice-to-3d-image/7586 "2025-06-30T15:25:45Z")
I have used itk::ImageFilter\, itk::Image\\> in C++ to convert a 2D slice to 3D volume in the past. I’m trying to achieve the same ends with itk.tile\_image\_filter with ITK Pyt… --- ## [reading and writng a dicom image](https://discourse.itk.org/t/reading-and-writng-a-dicom-image/3992)
**Author:** [@sarbabi](https://discourse.itk.org/u/sarbabi)\ **Replies:** 7\ **Last updated:** [June 26, 2025, 9:59pm UTC](https://discourse.itk.org/t/reading-and-writng-a-dicom-image/3992 "2025-06-26T21:59:06Z")
Hi, In the following simple piece of code I’m trying to read a DICOM image as sitkImage and its tags as a python dictionary. then I call another function to write that image in another location with the same tags readin… --- ## [Vector type single channel image](https://discourse.itk.org/t/vector-type-single-channel-image/7575)
**Author:** [@Franciska](https://discourse.itk.org/u/Franciska)\ **Replies:** 2\ **Last updated:** [June 25, 2025, 1:09pm UTC](https://discourse.itk.org/t/vector-type-single-channel-image/7575 "2025-06-25T13:09:54Z")
I have a dicom image thats shape is (1136, 852, 1) and PixelID is ‘vector of 8-bit unsigned integer’ . I want to cast this to float32 but as I can not cast vector type to simple float, following online advice I tried: … --- ## [Elastix WeightedCombinationTransform](https://discourse.itk.org/t/elastix-weightedcombinationtransform/7568)
**Author:** [@Sylvester\_Wu](https://discourse.itk.org/u/Sylvester_Wu)\ **Replies:** 2\ **Last updated:** [June 23, 2025, 4:14pm UTC](https://discourse.itk.org/t/elastix-weightedcombinationtransform/7568 "2025-06-23T16:14:45Z")
Hi Everyone, I’m very new to ITK and elastix. I have a set of 2-channel images of Tetraspeck fiducial beads in green and far red fluorescence and would like to register the two channels relative to each other for subseq… --- ## [Brain extraction - CT angiograms](https://discourse.itk.org/t/brain-extraction-ct-angiograms/7545)
**Author:** [@malar563](https://discourse.itk.org/u/malar563)\ **Replies:** 4\ **Last updated:** [May 28, 2025, 2:35pm UTC](https://discourse.itk.org/t/brain-extraction-ct-angiograms/7545 "2025-05-28T14:35:00Z")
Hi, I would like to automatically extract the brain from CT angiograms using a Python script. I have tested the WrapSolidify extension in 3D Slicer, and it works well (see screenshot). My questions are : 1 - How can I … --- ## [Is the rescale slope the same for all dicom in one sery?](https://discourse.itk.org/t/is-the-rescale-slope-the-same-for-all-dicom-in-one-sery/7546)
**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\ **Replies:** 1\ **Last updated:** [May 28, 2025, 2:08pm UTC](https://discourse.itk.org/t/is-the-rescale-slope-the-same-for-all-dicom-in-one-sery/7546 "2025-05-28T14:08:47Z")
Let’s say, one sery has 100 dicom files. Is the rescale slope (0028, 1053) must the same for all 100 dicom file? Or it may be different for dicom files in one sery? Any suggestion is appreciated~~~ --- ## [SimilarityIndexImageFilter (Beginner question)](https://discourse.itk.org/t/similarityindeximagefilter-beginner-question/7524)
**Author:** [@Mikko\_Pyysalo](https://discourse.itk.org/u/Mikko_Pyysalo)\ **Replies:** 2\ **Last updated:** [May 25, 2025, 6:40pm UTC](https://discourse.itk.org/t/similarityindeximagefilter-beginner-question/7524 "2025-05-25T18:40:23Z")
Dear community, I tried to compute the similarity of two binary labelmap volumes (pixel type unsigned char) in 3D Slicer Simple filters SimilarityIndexImageFilter. There comes an error message: Wrong number or type of … --- ## [ITKConfig.cmake problems](https://discourse.itk.org/t/itkconfig-cmake-problems/7520)
**Author:** [@Gio](https://discourse.itk.org/u/Gio)\ **Replies:** 3\ **Last updated:** [May 13, 2025, 6:21pm UTC](https://discourse.itk.org/t/itkconfig-cmake-problems/7520 "2025-05-13T18:21:49Z")
Hi all, I’m an absolute beginner :smiling\_face\_with\_tear:, trying to install “antspyx”, that require ITK. I’ve build ITK with CMake in Windows 11, now I’ve just one folder that i named “ITKbinaries” in C:/Users/giorg/bi… --- ## [Use an external SPM Displacement Field in SimpleITK to translate a point from the source MRI to the output MRI: Annotations not matching](https://discourse.itk.org/t/use-an-external-spm-displacement-field-in-simpleitk-to-translate-a-point-from-the-source-mri-to-the-output-mri-annotations-not-matching/7518)
**Author:** [@miaomiaomiao](https://discourse.itk.org/u/miaomiaomiao)\ **Replies:** 2\ **Last updated:** [May 13, 2025, 1:22pm UTC](https://discourse.itk.org/t/use-an-external-spm-displacement-field-in-simpleitk-to-translate-a-point-from-the-source-mri-to-the-output-mri-annotations-not-matching/7518 "2025-05-13T13:22:57Z")
Hello community, I have made point annotations in original MRIs and used SPM CAT12 to register the MRIs. Now I want to transform the points into the registered MRIs using SimpleITK. SPM CAT12 gives me a DisplacementFiel… --- ## [Scaling Problems with LandmarkBasedTransformInitializer](https://discourse.itk.org/t/scaling-problems-with-landmarkbasedtransforminitializer/7503)
**Author:** [@Rextorian](https://discourse.itk.org/u/Rextorian)\ **Replies:** 2\ **Last updated:** [April 25, 2025, 4:45pm UTC](https://discourse.itk.org/t/scaling-problems-with-landmarkbasedtransforminitializer/7503 "2025-04-25T16:45:39Z")
Hi, I am a little bit confused about the results I get from the LandmarkBasedTransformInitializer in combination with the similarity Transform. Lets say I have to sets of landmarks (points\_a and points\_b) where points\_… --- ## [MetaIO documentation](https://discourse.itk.org/t/metaio-documentation/7497)
**Author:** [@Francis](https://discourse.itk.org/u/Francis)\ **Replies:** 6\ **Last updated:** [April 16, 2025, 3:53pm UTC](https://discourse.itk.org/t/metaio-documentation/7497 "2025-04-16T15:53:25Z")
Hi all, I have just started working with MetaIO files and was hoping to look at the ITK documentation on the subject but when I attempt to access this site: https://itk.org/Wiki/ITK/MetaIO/Documentation I get 403 Forb… --- ## [similarity metrics in mono-modality registration](https://discourse.itk.org/t/similarity-metrics-in-mono-modality-registration/7493)
**Author:** [@blue\_sky](https://discourse.itk.org/u/blue_sky)\ **Replies:** 1\ **Last updated:** [April 13, 2025, 8:48pm UTC](https://discourse.itk.org/t/similarity-metrics-in-mono-modality-registration/7493 "2025-04-13T20:48:07Z")
Hi everyone. I am beginner in registration. The below code is part of the code related to SimpleITK Examples. It seems that this code is written for images with different modalities. But I want to register two CT images … --- ## [Release cuda memory](https://discourse.itk.org/t/release-cuda-memory/7491)
**Author:** [@langzhizhen](https://discourse.itk.org/u/langzhizhen)\ **Replies:** 2\ **Last updated:** [April 11, 2025, 12:38am UTC](https://discourse.itk.org/t/release-cuda-memory/7491 "2025-04-11T00:38:52Z")
Hello！ I would like to ask if there is a way to manually release cuda memory in RTK. I get “ITK ERROR: CUDA ERROR: out of memony” after running function “Update()” repeatedly. I want to manually release cuda memory that… --- ## [Points are not transformed correctly when using BSplineTransform](https://discourse.itk.org/t/points-are-not-transformed-correctly-when-using-bsplinetransform/7483)
**Author:** [@lukasz-migas](https://discourse.itk.org/u/lukasz-migas)\ **Replies:** 4\ **Last updated:** [March 31, 2025, 8:38am UTC](https://discourse.itk.org/t/points-are-not-transformed-correctly-when-using-bsplinetransform/7483 "2025-03-31T08:38:35Z")
Hi, I am looking for a bit of advice (or information on where I am going wrong) with regard to applying transformation to an image and coordinating points from GeoJSON. I have a composite transform consisting of 5 tran… --- ## [ForwardProjection about HU value](https://discourse.itk.org/t/forwardprojection-about-hu-value/7480)
**Author:** [@langzhizhen](https://discourse.itk.org/u/langzhizhen)\ **Replies:** 4\ **Last updated:** [March 29, 2025, 12:41pm UTC](https://discourse.itk.org/t/forwardprojection-about-hu-value/7480 "2025-03-29T12:41:24Z")
Hello, I have a question about the HU value. I input the data collected by CT, which is the real HU value. Is the pixel value of my reconstructed image also the real HU value? I see that the pixel values in the area outs… --- ## [Get \`numpy\` to \`SimpleITK\` data type mapping](https://discourse.itk.org/t/get-numpy-to-simpleitk-data-type-mapping/7479)
**Author:** [@jhlegarreta](https://discourse.itk.org/u/jhlegarreta)\ **Replies:** 13\ **Last updated:** [March 27, 2025, 4:04pm UTC](https://discourse.itk.org/t/get-numpy-to-simpleitk-data-type-mapping/7479 "2025-03-27T16:04:28Z")
Hi, is there a way to get the mapping of numpy data types to the SimpleITK data types? I have seen this, but it is a method variable, and it requires an input image. I am wondering whether I cant get the SimpleITK ty… --- ## [Bone being moved during deformable registration](https://discourse.itk.org/t/bone-being-moved-during-deformable-registration/7467)
**Author:** [@CrownMella](https://discourse.itk.org/u/CrownMella)\ **Replies:** 0\ **Last updated:** [March 18, 2025, 4:12pm UTC](https://discourse.itk.org/t/bone-being-moved-during-deformable-registration/7467 "2025-03-18T16:12:05Z")
Hi, I am currently using diffeomorphic demons (tried step length 0.5 and 2, included smoothupdatefield and smoothdisplacementfield) to register label maps, I noticed that even if a certain object remains stationary in b… --- ## [To v4 or not to v4](https://discourse.itk.org/t/to-v4-or-not-to-v4/7459)
**Author:** [@spinicist](https://discourse.itk.org/u/spinicist)\ **Replies:** 6\ **Last updated:** [March 17, 2025, 12:30pm UTC](https://discourse.itk.org/t/to-v4-or-not-to-v4/7459 "2025-03-17T12:30:46Z")
Hello, For a new project, are the “v4” versions of registration algorithms to be preferred over the ones without a suffix? Does the impending release of ITK 6 have any impact on this choice? I’ve been away from using IT… --- ## [ImageRegistrationMethodv4 crashes Unexpectedly](https://discourse.itk.org/t/imageregistrationmethodv4-crashes-unexpectedly/5268)
**Author:** [@autobuyer](https://discourse.itk.org/u/autobuyer)\ **Replies:** 1\ **Last updated:** [March 12, 2025, 4:12pm UTC](https://discourse.itk.org/t/imageregistrationmethodv4-crashes-unexpectedly/5268 "2025-03-12T16:12:01Z")
Hello, I am relatively new ITK user and I am trying to implement affine registration in C++. After going through examples, I was able to put together a reasonable solution. However, when I run it it crashes unexpectedly… --- ## [Unable to Read MHD Files with metaReadImage](https://discourse.itk.org/t/unable-to-read-mhd-files-with-metareadimage/7447)
**Author:** [@GMrrc](https://discourse.itk.org/u/GMrrc)\ **Replies:** 2\ **Last updated:** [February 28, 2025, 9:34pm UTC](https://discourse.itk.org/t/unable-to-read-mhd-files-with-metareadimage/7447 "2025-02-28T21:34:14Z")
Hello I’m encountering issues when trying to read MHD files using the metaReadImage method from ITK-Wasm. I’ve tried multiple approaches, but I cannot successfully load an MHD/ZRAW file. Additionally, the official onlin… --- ## [Real-time reconstruction](https://discourse.itk.org/t/real-time-reconstruction/7373)
**Author:** [@langzhizhen](https://discourse.itk.org/u/langzhizhen)\ **Replies:** 16\ **Last updated:** [February 27, 2025, 2:02am UTC](https://discourse.itk.org/t/real-time-reconstruction/7373 "2025-02-27T02:02:35Z")
Hello. I am now using Parker+FDK for CBCT. But right now I’m reconstructing 200 projected images by feeding them into the code, so I have to wait until the image is captured. Now I want to simulate the process of acquisi… --- ## [backprojection and forwardprojection about 2D image](https://discourse.itk.org/t/backprojection-and-forwardprojection-about-2d-image/7445)
**Author:** [@langzhizhen](https://discourse.itk.org/u/langzhizhen)\ **Replies:** 1\ **Last updated:** [February 22, 2025, 8:31am UTC](https://discourse.itk.org/t/backprojection-and-forwardprojection-about-2d-image/7445 "2025-02-22T08:31:37Z")
Hi. I want achieve NMAR algorithm recently, need to use the rtk.CudaBackProjectionImageFilter and rtk.CudaForwardProjectionImageFilter in 2 d image respectively. But there seems to be some issues with the image dimension… --- ## [About calculating FA(Fractional Anisotropy) with TensorRelativeAnisotropyImageFilter](https://discourse.itk.org/t/about-calculating-fa-fractional-anisotropy-with-tensorrelativeanisotropyimagefilter/7437)
**Author:** [@Pinyu\_Huang](https://discourse.itk.org/u/Pinyu_Huang)\ **Replies:** 0\ **Last updated:** [February 18, 2025, 8:07am UTC](https://discourse.itk.org/t/about-calculating-fa-fractional-anisotropy-with-tensorrelativeanisotropyimagefilter/7437 "2025-02-18T08:07:08Z")
Hi there, I tried to calculate FA and PDD for streamlines tractography with TensorRelativeAnisotropyImageFilter. And I basically follow the workflow in the website (ITK: Examples/Filtering/DiffusionTensor3DReconstructio… --- ## [\[SOLVED\] Difficulty getting registration to work with mask on moving image](https://discourse.itk.org/t/solved-difficulty-getting-registration-to-work-with-mask-on-moving-image/7423)
**Author:** [@ebaudrez](https://discourse.itk.org/u/ebaudrez)\ **Replies:** 5\ **Last updated:** [February 6, 2025, 1:37pm UTC](https://discourse.itk.org/t/solved-difficulty-getting-registration-to-work-with-mask-on-moving-image/7423 "2025-02-06T13:37:06Z")
Update 6 February: I got this to work. I confirm the mask on the moving image works. Hello! I am having difficulty to get a registration with a mask on the moving image to work. I have attached the full code below, as w… --- ## [Writing and reading .tif metadata](https://discourse.itk.org/t/writing-and-reading-tif-metadata/7419)
**Author:** [@rhysgt](https://discourse.itk.org/u/rhysgt)\ **Replies:** 2\ **Last updated:** [February 4, 2025, 6:15pm UTC](https://discourse.itk.org/t/writing-and-reading-tif-metadata/7419 "2025-02-04T18:15:52Z")
I am reading an image with imread: out\_image = itk.imread(files\[0\], itk.UC) then changing adding metadata tags: out\_image\['TileWidth'\] = str(int(size\[0\])) out\_image\['Date\_start'\] = other\_image\['Date'\] When I run prin… --- ## [ITK vs PyTorch calculation for Mutual Information](https://discourse.itk.org/t/itk-vs-pytorch-calculation-for-mutual-information/7365)
**Author:** [@thanuja](https://discourse.itk.org/u/thanuja)\ **Replies:** 3\ **Last updated:** [January 31, 2025, 2:41pm UTC](https://discourse.itk.org/t/itk-vs-pytorch-calculation-for-mutual-information/7365 "2025-01-31T14:41:06Z")
Hi All, I’m calculating the mutual information metric value between two 3D images using ITK and PyTorch and getting two different values for the same bin size. The sample values are (ITK and Pytorch): 0.53140919429619… --- ## [Why is ITK running slower in C++ than in python?](https://discourse.itk.org/t/why-is-itk-running-slower-in-c-than-in-python/7394)
**Author:** [@LuOSS](https://discourse.itk.org/u/LuOSS)\ **Replies:** 4\ **Last updated:** [January 30, 2025, 7:55pm UTC](https://discourse.itk.org/t/why-is-itk-running-slower-in-c-than-in-python/7394 "2025-01-30T19:55:44Z")
I have written a small program in python where a combination of morphology, masking and gaussian filters are applied to a 3D image. It is made with numpy arrays and scipy functions but I thought to use a dedicated image … --- ## [Registration of MRI and Ultrasound volumes](https://discourse.itk.org/t/registration-of-mri-and-ultrasound-volumes/7410)
**Author:** [@Sanjith\_T](https://discourse.itk.org/u/Sanjith_T)\ **Replies:** 0\ **Last updated:** [January 28, 2025, 6:55am UTC](https://discourse.itk.org/t/registration-of-mri-and-ultrasound-volumes/7410 "2025-01-28T06:55:41Z")
Hello Everyone, I’m new to registration and I want to register 3D ultrasound with 3D MRI from the BITE Dataset using ITK. Any insights on where to start or any examples would be very helpful. As the transformations with… --- ## [Motion modeling in-between frames via deformation fields](https://discourse.itk.org/t/motion-modeling-in-between-frames-via-deformation-fields/6538)
**Author:** [@Darius\_Grazulis](https://discourse.itk.org/u/Darius_Grazulis)\ **Replies:** 8\ **Last updated:** [January 24, 2025, 6:32pm UTC](https://discourse.itk.org/t/motion-modeling-in-between-frames-via-deformation-fields/6538 "2025-01-24T18:32:28Z")
Hello, I would like to ask for some guidance on how it would be possible to use deformation fields acquired from groupwise (or pairwise) registration to model (interpolate/simulate) the motion in-between frames. Data t… --- ## [projection images config](https://discourse.itk.org/t/projection-images-config/7380)
**Author:** [@langzhizhen](https://discourse.itk.org/u/langzhizhen)\ **Replies:** 11\ **Last updated:** [January 16, 2025, 1:38pm UTC](https://discourse.itk.org/t/projection-images-config/7380 "2025-01-16T13:38:41Z")
Hello. I’m currently performing a CT reconstruction using FDK. This process involves the setting of projection and the setting of reconstructed data. How should the origin, spacing and size of these two parts be set? Cur… [Previous page](https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false) [Next page](https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=2)