# Beginner Questions

**URL:** https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=3

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**Page:** 4

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## [3D Registration Problem - Resulting Image truncated after the resampling](https://discourse.itk.org/t/3d-registration-problem-resulting-image-truncated-after-the-resampling/7156)

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**Author:** [@Bigfahma](https://discourse.itk.org/u/Bigfahma)\
**Replies:** 3\
**Last updated:** [August 9, 2024, 3:25pm UTC](https://discourse.itk.org/t/3d-registration-problem-resulting-image-truncated-after-the-resampling/7156 "2024-08-09T15:25:54Z")

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Hi all, I’ve been struggling with a 3D image registration issue for weeks, and I find myself with more questions than answers. I’m working on registering 3D microCT images of bones to analyze their evolution over time f…

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## [3D Reconstruction from 2D XRay DICOM images](https://discourse.itk.org/t/3d-reconstruction-from-2d-xray-dicom-images/7161)

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**Author:** [@drathin4](https://discourse.itk.org/u/drathin4)\
**Replies:** 2\
**Last updated:** [August 8, 2024, 2:13pm UTC](https://discourse.itk.org/t/3d-reconstruction-from-2d-xray-dicom-images/7161 "2024-08-08T14:13:35Z")

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Can we reconstruct 3D model from 2D DiCoM images obtained from XRays? I read this link, but didn’t find any relevant answer: 3D reconstruction I also didn’t find any geometric metadata in the XRay DiCoM files unlike t…

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## [Which filter to use to convert from 16 bit image to 8 bit Image](https://discourse.itk.org/t/which-filter-to-use-to-convert-from-16-bit-image-to-8-bit-image/7158)

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**Author:** [@imikejackson](https://discourse.itk.org/u/imikejackson)\
**Replies:** 1\
**Last updated:** [August 7, 2024, 6:38pm UTC](https://discourse.itk.org/t/which-filter-to-use-to-convert-from-16-bit-image-to-8-bit-image/7158 "2024-08-07T18:38:56Z")

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Sort of having a brain fart today but what is the ITK Filter I am looking for that would change from a 16 bit image to an 8 bit image? is that a simple ITKImageCast? I feel like that isn’t correct because if I have value…

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## [Use masks for registration in itk-elastix](https://discourse.itk.org/t/use-masks-for-registration-in-itk-elastix/7051)

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**Author:** [@cousin](https://discourse.itk.org/u/cousin)\
**Replies:** 2\
**Last updated:** [August 7, 2024, 4:05pm UTC](https://discourse.itk.org/t/use-masks-for-registration-in-itk-elastix/7051 "2024-08-07T16:05:57Z")

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Greetings to everyone, I am discovering itk-elastix in python (module loaded as itk) and I am starting to use itk.elastix\_registration\_method I could not find the signature of this function but managed to grab some inf…

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## [Interpolating vector image with itk python](https://discourse.itk.org/t/interpolating-vector-image-with-itk-python/7152)

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**Author:** [@wkacct\_acctwk](https://discourse.itk.org/u/wkacct_acctwk)\
**Replies:** 4\
**Last updated:** [August 7, 2024, 2:59pm UTC](https://discourse.itk.org/t/interpolating-vector-image-with-itk-python/7152 "2024-08-07T14:59:30Z")

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I am currently trying to get the interpolated vector at a subpixel location using the itk.LinearInterpolateImageFunction in python. It was my understanding that this function is supposed to support both vector and scalar…

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## [What is problem with conversion from nifti file to vtp](https://discourse.itk.org/t/what-is-problem-with-conversion-from-nifti-file-to-vtp/7154)

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**Author:** [@babayka](https://discourse.itk.org/u/babayka)\
**Replies:** 0\
**Last updated:** [August 7, 2024, 4:10am UTC](https://discourse.itk.org/t/what-is-problem-with-conversion-from-nifti-file-to-vtp/7154 "2024-08-07T04:10:51Z")

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I have code that utilizes vtp and nibabel to convert read nifti file into vtp then I check how the geometry was made for vasculature through GeometryViewer of vtp examples. import nibabel as nib import vtk from vtkmodul…

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## [Order of elements in a displacement field](https://discourse.itk.org/t/order-of-elements-in-a-displacement-field/7148)

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**Author:** [@koegl](https://discourse.itk.org/u/koegl)\
**Replies:** 1\
**Last updated:** [August 1, 2024, 1:19pm UTC](https://discourse.itk.org/t/order-of-elements-in-a-displacement-field/7148 "2024-08-01T13:19:03Z")

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Let’s say I have a displacement field in SimpleITK of the shape 100,100,100,3. are the components of the displacement at each voxel (x,y,z) or (z,y,x)?

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## [Compute eigen vectors from 3D Hessian matrix in Python](https://discourse.itk.org/t/compute-eigen-vectors-from-3d-hessian-matrix-in-python/7134)

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**Author:** [@Maolin](https://discourse.itk.org/u/Maolin)\
**Replies:** 1\
**Last updated:** [July 31, 2024, 2:57pm UTC](https://discourse.itk.org/t/compute-eigen-vectors-from-3d-hessian-matrix-in-python/7134 "2024-07-31T14:57:10Z")

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Hi all, I saw the function itk.SymmetricEigenAnalysisImageFilter can compute the eigen values from a hessian image, but I didn’t see a function that could compute te eigen vectors from a hessian image. Could you help me…

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## [Jacobian determinant - 2D deformation field and pixel/voxel spacing?](https://discourse.itk.org/t/jacobian-determinant-2d-deformation-field-and-pixel-voxel-spacing/7145)

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**Author:** [@lbrandao](https://discourse.itk.org/u/lbrandao)\
**Replies:** 1\
**Last updated:** [July 31, 2024, 11:59am UTC](https://discourse.itk.org/t/jacobian-determinant-2d-deformation-field-and-pixel-voxel-spacing/7145 "2024-07-31T11:59:32Z")

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Dear all, I have a numpy array representing a deformation field with 2D shape (i.e., only x and y displacements), and I want to compute its Jacobian determinant. Here’s how I’m doing it: def\_field\_np is a numpy array …

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## [How to create vtp file from nrrd file for further geometry view?](https://discourse.itk.org/t/how-to-create-vtp-file-from-nrrd-file-for-further-geometry-view/7141)

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**Author:** [@babayka](https://discourse.itk.org/u/babayka)\
**Replies:** 4\
**Last updated:** [July 31, 2024, 11:44am UTC](https://discourse.itk.org/t/how-to-create-vtp-file-from-nrrd-file-for-further-geometry-view/7141 "2024-07-31T11:44:45Z")

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I am new to both itk/vtk and currently would like to display a 3d render of the vtp file of brain taken converted from nrrd/nifti file, where the final render will be shown in frontend using javascript(react), and the co…

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## [Build and install SimpleITK with SimpleITK\_USE\_ELASTIX option in linux environment](https://discourse.itk.org/t/build-and-install-simpleitk-with-simpleitk-use-elastix-option-in-linux-environment/7128)

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**Author:** [@thanuja](https://discourse.itk.org/u/thanuja)\
**Replies:** 8\
**Last updated:** [July 29, 2024, 1:11pm UTC](https://discourse.itk.org/t/build-and-install-simpleitk-with-simpleitk-use-elastix-option-in-linux-environment/7128 "2024-07-29T13:11:28Z")

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Hi All, I’m trying to install simple elastix package using SimpleITK v2.2.1 source code in a python 3.10.13 virtual environment by following the documentation:https://simpleitk.readthedocs.io/en/master/building.html I’…

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## [How to extract blood vessel's orientation in Python?](https://discourse.itk.org/t/how-to-extract-blood-vessels-orientation-in-python/7127)

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**Author:** [@Maolin](https://discourse.itk.org/u/Maolin)\
**Replies:** 2\
**Last updated:** [July 28, 2024, 7:34pm UTC](https://discourse.itk.org/t/how-to-extract-blood-vessels-orientation-in-python/7127 "2024-07-28T19:34:59Z")

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Hi all, I am new to ITK and I’d like to look for a way to use simpleITk or Python ITK to extract the blood vessel’s orientation. I reviewd the function itk.hessian\_recursive\_gaussian\_image\_filter that can compute the h…

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## [Is better to use \`itk.imread(dir)\` than \`itk.imread(file\_list)\`?](https://discourse.itk.org/t/is-better-to-use-itk-imread-dir-than-itk-imread-file-list/7123)

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**Author:** [@jinquan\_guan](https://discourse.itk.org/u/jinquan_guan)\
**Replies:** 6\
**Last updated:** [July 25, 2024, 2:21pm UTC](https://discourse.itk.org/t/is-better-to-use-itk-imread-dir-than-itk-imread-file-list/7123 "2024-07-25T14:21:43Z")

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I made an experiment about the itk.imread function, and found something interesting. I putted .dcm files with the same series ID in a directory. And then convert the dicom data into nii.gz format. Here come the differen…

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## [How to pass double\* of C++ in python?](https://discourse.itk.org/t/how-to-pass-double-of-c-in-python/6716)

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**Author:** [@guo7212](https://discourse.itk.org/u/guo7212)\
**Replies:** 3\
**Last updated:** [July 25, 2024, 7:26am UTC](https://discourse.itk.org/t/how-to-pass-double-of-c-in-python/6716 "2024-07-25T07:26:00Z")

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Hi all, I tried to use itk-python. There is a function in itk::PointSet, which has a parameter of double\* in C++. I want to know how to set it in Python. The error message is as follows: TypeError: in method 'itkPointS…

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## [How to extract multiple components image from dicom series?](https://discourse.itk.org/t/how-to-extract-multiple-components-image-from-dicom-series/7097)

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**Author:** [@jinquan\_guan](https://discourse.itk.org/u/jinquan_guan)\
**Replies:** 5\
**Last updated:** [July 23, 2024, 2:53pm UTC](https://discourse.itk.org/t/how-to-extract-multiple-components-image-from-dicom-series/7097 "2024-07-23T14:53:31Z")

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The dicom files can be correctly recognized as multiple components image by ITK-SNAP: The proof is : I can change the component/view of the dicom file: But when I extract nii.gz file from the dicom series, the vi…

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## [Difference between SimpleElastix and ITKElastix](https://discourse.itk.org/t/difference-between-simpleelastix-and-itkelastix/6658)

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**Author:** [@l.mejivar](https://discourse.itk.org/u/l.mejivar)\
**Replies:** 3\
**Last updated:** [July 19, 2024, 6:47pm UTC](https://discourse.itk.org/t/difference-between-simpleelastix-and-itkelastix/6658 "2024-07-19T18:47:15Z")

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Hello, I am writing a script to register (non-rigid) several thousands of images. I noticed that SimpleElastix is integrated and ITK, but the original repository was archived. I also noticed that there is a different op…

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## [error LNK2005: \_\_ ucrt \_ int \_ to \_ float has been defined in itktiff-6.0.lib (tif\_ aux.obj)](https://discourse.itk.org/t/error-lnk2005-ucrt-int-to-float-has-been-defined-in-itktiff-6-0-lib-tif-aux-obj/7073)

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**Author:** [@xiaohua](https://discourse.itk.org/u/xiaohua)\
**Replies:** 6\
**Last updated:** [July 19, 2024, 12:56am UTC](https://discourse.itk.org/t/error-lnk2005-ucrt-int-to-float-has-been-defined-in-itktiff-6-0-lib-tif-aux-obj/7073 "2024-07-19T00:56:57Z")

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error LNK2005: \_\_ ucrt \_ int \_ to \_ float has been defined in itktiff-6.0.lib (tif\_ aux.obj)

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## [TransformPoint and resampling images](https://discourse.itk.org/t/transformpoint-and-resampling-images/6713)

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**Author:** [@Snaype1](https://discourse.itk.org/u/Snaype1)\
**Replies:** 4\
**Last updated:** [July 15, 2024, 1:19pm UTC](https://discourse.itk.org/t/transformpoint-and-resampling-images/6713 "2024-07-15T13:19:09Z")

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Hello, I am using SimpleITK (python) and try to understand how the registration framework operates. Once the alignment is done (in my case using L-BFGS-B optimizer, correlation as similarity metric, BsplineTransform an…

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## [Motion correction for 4D brain image (DTI and fMRI)](https://discourse.itk.org/t/motion-correction-for-4d-brain-image-dti-and-fmri/7048)

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**Author:** [@Sunita\_Patel](https://discourse.itk.org/u/Sunita_Patel)\
**Replies:** 1\
**Last updated:** [July 11, 2024, 12:44pm UTC](https://discourse.itk.org/t/motion-correction-for-4d-brain-image-dti-and-fmri/7048 "2024-07-11T12:44:38Z")

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Dear ITK members, We want to perform motion correction in 4D brain image such as DTI and fMRI. Is it fine to register the series of 3D brain volume on the first 3D image or b0 (baseline) MRI image in case DTI? or Any ad…

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## [Convert .nii.gz warp to .h5 (with proper header)](https://discourse.itk.org/t/convert-nii-gz-warp-to-h5-with-proper-header/6673)

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**Author:** [@smeisler](https://discourse.itk.org/u/smeisler)\
**Replies:** 10\
**Last updated:** [July 10, 2024, 8:08pm UTC](https://discourse.itk.org/t/convert-nii-gz-warp-to-h5-with-proper-header/6673 "2024-07-10T20:08:11Z")

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Hi! I have been modifying an anatomical processing workflow that largely uses ANTs. I have been trying to incorporate FreeSurfer’s synthmorph to calculate a registration, which outputs in RAS convention. I have been abl…

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## [ITK or SimpleITK in Python?](https://discourse.itk.org/t/itk-or-simpleitk-in-python/2926)

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**Author:** [@mridev](https://discourse.itk.org/u/mridev)\
**Replies:** 13\
**Last updated:** [July 10, 2024, 2:30am UTC](https://discourse.itk.org/t/itk-or-simpleitk-in-python/2926 "2024-07-10T02:30:24Z")

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Hi all, I know this question has been asked before. I have started developing commercial solutions for medical image analysis in python. I have used both ITK and SimpleITK but would like to use only one of them. It seem…

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## [TriangleMeshToBinaryImageFilter In Python](https://discourse.itk.org/t/trianglemeshtobinaryimagefilter-in-python/1604)

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**Author:** [@rogertrullo](https://discourse.itk.org/u/rogertrullo)\
**Replies:** 24\
**Last updated:** [July 10, 2024, 2:25am UTC](https://discourse.itk.org/t/trianglemeshtobinaryimagefilter-in-python/1604 "2024-07-10T02:25:00Z")

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Hi, I’m trying to get a 3D binary image from a mesh stl file. I found an example in c++ using the TriangleMeshToBinaryImageFilter function. I was wondering if this function is available from the Python interface? Thanks…

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## [Unable to compile simpleRTK](https://discourse.itk.org/t/unable-to-compile-simplertk/6723)

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**Author:** [@xem123](https://discourse.itk.org/u/xem123)\
**Replies:** 8\
**Last updated:** [July 6, 2024, 11:22am UTC](https://discourse.itk.org/t/unable-to-compile-simplertk/6723 "2024-07-06T11:22:09Z")

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Hello, I want to use simpleRTK in Python. I saw on the official website that I need to compile the ITK library first, then the RTK library, and check the BUILD\_SIMPLERTK option; but now the RTK library doesn’t support se…

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## [no itk.join\_image\_filter in ITK 5.1.2](https://discourse.itk.org/t/no-itk-join-image-filter-in-itk-5-1-2/3671)

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**Author:** [@dyoll](https://discourse.itk.org/u/dyoll)\
**Replies:** 8\
**Last updated:** [July 2, 2024, 5:03am UTC](https://discourse.itk.org/t/no-itk-join-image-filter-in-itk-5-1-2/3671 "2024-07-02T05:03:49Z")

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It seems the itk::JoinImageFilter is not wrapped to python (yet). I could not find it in the 5.1.2 release. Is there a list of filters which have been wrapped? I would expect a class named itk.join\_image\_filter. The on…

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## [Is Dark Mode Available?](https://discourse.itk.org/t/is-dark-mode-available/6724)

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**Author:** [@blowekamp](https://discourse.itk.org/u/blowekamp)\
**Replies:** 3\
**Last updated:** [June 27, 2024, 2:57pm UTC](https://discourse.itk.org/t/is-dark-mode-available/6724 "2024-06-27T14:57:52Z")

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Is Dark Mode available for ITK Discourse? It is coming up by default for other discourse servers like 3D Slicer, but not here and I don’t see a setting any place.

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## [It is impossible to perform the fast Fourier transform on the image.](https://discourse.itk.org/t/it-is-impossible-to-perform-the-fast-fourier-transform-on-the-image/6717)

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**Author:** [@xem123](https://discourse.itk.org/u/xem123)\
**Replies:** 6\
**Last updated:** [June 27, 2024, 12:04pm UTC](https://discourse.itk.org/t/it-is-impossible-to-perform-the-fast-fourier-transform-on-the-image/6717 "2024-06-27T12:04:50Z")

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Hi all: question：I want to use the functions “itk::RealToHalfHermitianForwardFFTImageFilter” in ITK version 5.3 to perform fast Fourier transform and filtering on the image. However, an error occurred after I input an i…

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## [Temporal Dimension Semantics in 2D + Time Image Series Written Out As 3D Image](https://discourse.itk.org/t/temporal-dimension-semantics-in-2d-time-image-series-written-out-as-3d-image/6708)

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**Author:** [@constantine](https://discourse.itk.org/u/constantine)\
**Replies:** 8\
**Last updated:** [June 25, 2024, 4:59am UTC](https://discourse.itk.org/t/temporal-dimension-semantics-in-2d-time-image-series-written-out-as-3d-image/6708 "2024-06-25T04:59:15Z")

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Hello Everyone, Given a bunch of 2D frames in a temporal series, what is the intended way in ITK to write those out to be recognised as 2D + t image, not just as 3D image? I’m asking because ITK-Snap or Slicer display …

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## [Cancel ElastixImageFilter.Execute()](https://discourse.itk.org/t/cancel-elastiximagefilter-execute/6634)

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**Author:** [@G\_Y](https://discourse.itk.org/u/G_Y)\
**Replies:** 2\
**Last updated:** [June 20, 2024, 9:45pm UTC](https://discourse.itk.org/t/cancel-elastiximagefilter-execute/6634 "2024-06-20T21:45:51Z")

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Hi, I have a program that sets up and calls ElastixImageFilter.Execute() from SimpleITK library when the user clicks the “Apply” button, it works fine, however sometimes the user changes mind and wants to cancel the on-g…

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## [Interpolating Between Stack of Images in 3D Slicer](https://discourse.itk.org/t/interpolating-between-stack-of-images-in-3d-slicer/6703)

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**Author:** [@valerie](https://discourse.itk.org/u/valerie)\
**Replies:** 4\
**Last updated:** [June 19, 2024, 2:59pm UTC](https://discourse.itk.org/t/interpolating-between-stack-of-images-in-3d-slicer/6703 "2024-06-19T14:59:42Z")

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Hi, I am trying to interpolate between a stack of 2D ultrasound images using multiple methods for comparison (i.e. Gaussian Kernel, Nearest Neighbor, Linear, etc.) in 3D Slicer. I posted a question in the 3D Slicer comm…

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## [GDCMSeriesFileNames fails to read folder with non ascii characters](https://discourse.itk.org/t/gdcmseriesfilenames-fails-to-read-folder-with-non-ascii-characters/2365)

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**Author:** [@antoine.letouzey](https://discourse.itk.org/u/antoine.letouzey)\
**Replies:** 13\
**Last updated:** [June 17, 2024, 9:30pm UTC](https://discourse.itk.org/t/gdcmseriesfilenames-fails-to-read-folder-with-non-ascii-characters/2365 "2024-06-17T21:30:32Z")

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I’m having trouble with code that worked just fine for years. I’m trying to open a DICOM dataset from Japan and my code cannot see any files of the series folder. The code is (with placeholders for seriesUID and patient…

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