# Uncategorized

**URL:** https://discourse.itk.org/c/uncategorized/1.md?no_subcategories=false&page=13

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

**Page:** 14

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## [\<unknown\> Unknown/Unhandle MediaStorage, but Pixel Data element found](https://discourse.itk.org/t/unknown-unknown-unhandle-mediastorage-but-pixel-data-element-found/1693)

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**Author:** [@zandarina](https://discourse.itk.org/u/zandarina)\
**Replies:** 3\
**Last updated:** [March 21, 2019, 6:56pm UTC](https://discourse.itk.org/t/unknown-unknown-unhandle-mediastorage-but-pixel-data-element-found/1693 "2019-03-21T18:56:38Z")

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Dear all, everytime i write the output of a filter, i get this warning. It doesn´t throw any error, and it writes well, but it is a bit annoying to get this warning as an output for each slice as i like to follow the ou…

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## [World coordinate do not give me the correct dicom coordinate](https://discourse.itk.org/t/world-coordinate-do-not-give-me-the-correct-dicom-coordinate/1644)

<div class="topic-metadata">

**Author:** [@zandarina](https://discourse.itk.org/u/zandarina)\
**Replies:** 12\
**Last updated:** [March 21, 2019, 12:25pm UTC](https://discourse.itk.org/t/world-coordinate-do-not-give-me-the-correct-dicom-coordinate/1644 "2019-03-21T12:25:41Z")

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Dear all, I use itk to perform 2d segmentation of a 3d volume given by a dicom series and i need to add some seeds with the mouse for some 2d slices. So i am forced to show a 2d slice in vtk obtained with itk (using e…

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## [Numpy vnl bridge unexpected behavior](https://discourse.itk.org/t/numpy-vnl-bridge-unexpected-behavior/1659)

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**Author:** [@simon.rit](https://discourse.itk.org/u/simon.rit)\
**Replies:** 7\
**Last updated:** [March 20, 2019, 8:48am UTC](https://discourse.itk.org/t/numpy-vnl-bridge-unexpected-behavior/1659 "2019-03-20T08:48:03Z")

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Hi, I tend to write too many things on the same line in Python and this caused an unexpected behavior for the numpy vnl bridge. It occurred in a different context but I have the following minimal example import itk …

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## [Getting an interpolated image based on sparse pixel values](https://discourse.itk.org/t/getting-an-interpolated-image-based-on-sparse-pixel-values/1682)

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**Author:** [@sedghi](https://discourse.itk.org/u/sedghi)\
**Replies:** 10\
**Last updated:** [March 19, 2019, 2:50pm UTC](https://discourse.itk.org/t/getting-an-interpolated-image-based-on-sparse-pixel-values/1682 "2019-03-19T14:50:56Z")

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Lets assume that we have a 3D image of size 100x100x100, and we only want to set pixel values for 1000 locations in this 3D image. Is it possible to get the interpolated image based on these sparse pixel values? which fi…

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## ['add' bynary mask to a volume](https://discourse.itk.org/t/add-bynary-mask-to-a-volume/1676)

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**Author:** [@Marco\_Festugato](https://discourse.itk.org/u/Marco_Festugato)\
**Replies:** 1\
**Last updated:** [March 15, 2019, 7:49pm UTC](https://discourse.itk.org/t/add-bynary-mask-to-a-volume/1676 "2019-03-15T19:49:45Z")

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Hi guys! I have to segment the liver vessels from a volume and ‘highlight’ them so they are more visible. I thought of creating a binary volume of my vessels and ‘add’ it to my volume…do u have any suggestions/examples/c…

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## [Is itk able to preserve the VOI LUT, windows level.. to use vtk afterwards with all the info](https://discourse.itk.org/t/is-itk-able-to-preserve-the-voi-lut-windows-level-to-use-vtk-afterwards-with-all-the-info/1671)

<div class="topic-metadata">

**Author:** [@zandarina](https://discourse.itk.org/u/zandarina)\
**Replies:** 1\
**Last updated:** [March 15, 2019, 1:27pm UTC](https://discourse.itk.org/t/is-itk-able-to-preserve-the-voi-lut-windows-level-to-use-vtk-afterwards-with-all-the-info/1671 "2019-03-15T13:27:52Z")

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Dear all, I have to perform some segmentation and visualize it in vtk. I wonder if i read the dicom series in itk first, i wonder if it will lose the voi lut, windows level to show in vtk. So my question is if itk pre…

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## [LabelGeometryImageFilterType linkage errors when definition](https://discourse.itk.org/t/labelgeometryimagefiltertype-linkage-errors-when-definition/1653)

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**Author:** [@zandarina](https://discourse.itk.org/u/zandarina)\
**Replies:** 1\
**Last updated:** [March 12, 2019, 2:25pm UTC](https://discourse.itk.org/t/labelgeometryimagefiltertype-linkage-errors-when-definition/1653 "2019-03-12T14:25:14Z")

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Dear all, I would like to detect circular shapes and knwo the features to select the one i am interested in a fast way and i would like to use this labelgeometryImageFilterType to obtain for example the eccentricity of…

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## [The collapse of the dimension using extractFilter does not make sense](https://discourse.itk.org/t/the-collapse-of-the-dimension-using-extractfilter-does-not-make-sense/1642)

<div class="topic-metadata">

**Author:** [@zandarina](https://discourse.itk.org/u/zandarina)\
**Replies:** 3\
**Last updated:** [March 9, 2019, 7:37pm UTC](https://discourse.itk.org/t/the-collapse-of-the-dimension-using-extractfilter-does-not-make-sense/1642 "2019-03-09T19:37:56Z")

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Dear all, I want to do 3d segmentation of an especific vessel but i am having a lot of problems with memory with the 3d filters as this vessels has no contrast at all and i do not have any prior info only intensities an…

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## [MEMORY ALLOCATION error](https://discourse.itk.org/t/memory-allocation-error/1639)

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**Author:** [@zandarina](https://discourse.itk.org/u/zandarina)\
**Replies:** 2\
**Last updated:** [March 7, 2019, 5:21pm UTC](https://discourse.itk.org/t/memory-allocation-error/1639 "2019-03-07T17:21:04Z")

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Dear all, I try this function for vessel segmentation but it get an error of bad memory allocation. I see it is not a streaming funcion. Is there any way to use it without resizing my volume?. Thanks using HessianFilt…

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## [itkSimpleFuzzyConnectednessImageFilterBase](https://discourse.itk.org/t/itksimplefuzzyconnectednessimagefilterbase/1636)

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**Author:** [@zandarina](https://discourse.itk.org/u/zandarina)\
**Replies:** 1\
**Last updated:** [March 6, 2019, 2:52pm UTC](https://discourse.itk.org/t/itksimplefuzzyconnectednessimagefilterbase/1636 "2019-03-06T14:52:45Z")

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Dear all, I want to use this fucntion: itkSimpleFuzzyConnectednessImageFilterBase but it does no appear in the new version. There is anyway to use fuzzy connectness in the new versions? Thanks

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## [dicom + Hessian filter](https://discourse.itk.org/t/dicom-hessian-filter/1631)

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**Author:** [@zandarina](https://discourse.itk.org/u/zandarina)\
**Replies:** 1\
**Last updated:** [March 4, 2019, 2:04pm UTC](https://discourse.itk.org/t/dicom-hessian-filter/1631 "2019-03-04T14:04:00Z")

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Hi i want to read series of dicom and apply the hessian filter but i get an error when i use hessianFilter-\>SetInput(reader-\>GetInput()); because it does not accept a reader of series of dicoms. I have read the dicom…

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## [Handling of combined accents by ITK system tools](https://discourse.itk.org/t/handling-of-combined-accents-by-itk-system-tools/1619)

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**Author:** [@tim-evain](https://discourse.itk.org/u/tim-evain)\
**Replies:** 11\
**Last updated:** [February 28, 2019, 3:09pm UTC](https://discourse.itk.org/t/handling-of-combined-accents-by-itk-system-tools/1619 "2019-02-28T15:09:13Z")

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Hello everyone, I’m using the itksys tools to do some file parsing and I’ve encountered a nasty problem with some filepaths containing accented characters. For example I have this folder name in my database : “aorte\_dé…

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## [Shadowed functions in GPUImage (or CudaImage)](https://discourse.itk.org/t/shadowed-functions-in-gpuimage-or-cudaimage/1614)

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**Author:** [@simon.rit](https://discourse.itk.org/u/simon.rit)\
**Replies:** 5\
**Last updated:** [February 25, 2019, 3:16pm UTC](https://discourse.itk.org/t/shadowed-functions-in-gpuimage-or-cudaimage/1614 "2019-02-25T15:16:32Z")

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I am looking for explanations and advices, I hope you can help. I would like to be able to Graft an itk::Image to an itk::CudaImage (which is similar to itk::GPUImage). Recently, I have removed some code in itk::CudaImag…

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## [Reproducibility of image registration](https://discourse.itk.org/t/reproducibility-of-image-registration/1591)

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**Author:** [@take5v](https://discourse.itk.org/u/take5v)\
**Replies:** 7\
**Last updated:** [February 22, 2019, 1:59pm UTC](https://discourse.itk.org/t/reproducibility-of-image-registration/1591 "2019-02-22T13:59:45Z")

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Hi, I’ve done the registration of microscopical images with affine transform using conjugate gradient line search. I observe small to a large variation in the results after several complete the same runs. Metric is Matt…

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## [Imaging archives](https://discourse.itk.org/t/imaging-archives/1572)

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**Author:** [@hadasara](https://discourse.itk.org/u/hadasara)\
**Replies:** 2\
**Last updated:** [February 11, 2019, 4:56pm UTC](https://discourse.itk.org/t/imaging-archives/1572 "2019-02-11T16:56:16Z")

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Hi all, I’m looking for an imaging archive to test my algorithms, that store both MRI and CT scans, of the same patient, specifically brain GBM patients. I know the TCIA archive. Any other suggestions? Thank you, Ha…

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## [Use EuclideanDistancePointMetric in python itk](https://discourse.itk.org/t/use-euclideandistancepointmetric-in-python-itk/1490)

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**Author:** [@Roulbac](https://discourse.itk.org/u/Roulbac)\
**Replies:** 5\
**Last updated:** [January 3, 2019, 6:29pm UTC](https://discourse.itk.org/t/use-euclideandistancepointmetric-in-python-itk/1490 "2019-01-03T18:29:05Z")

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Hi all, I need to use the EuclideanDistancePointMetric but it does not come with PyPi’s itk. I tried compiling itk with Python wrapping but I can’t find the build configuration that wraps that class, which belongs to R…

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## [Accessing a possibly non-existent function in a ImageFileReader object](https://discourse.itk.org/t/accessing-a-possibly-non-existent-function-in-a-imagefilereader-object/1462)

<div class="topic-metadata">

**Author:** [@gdevenyi](https://discourse.itk.org/u/gdevenyi)\
**Replies:** 5\
**Last updated:** [December 6, 2018, 10:25pm UTC](https://discourse.itk.org/t/accessing-a-possibly-non-existent-function-in-a-imagefilereader-object/1462 "2018-12-06T22:25:59Z")

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Suppose that I create reader based ImageFileReader, and I want to do reader-\>SetX(true). But depending upon the file that was passed into ImageFileReader, “SetX” might not exist. Is it possible to get this to work wit…

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## [How to convert a anisotropic to isotropic and then back to anisotropic?](https://discourse.itk.org/t/how-to-convert-a-anisotropic-to-isotropic-and-then-back-to-anisotropic/1451)

<div class="topic-metadata">

**Author:** [@mark\_john](https://discourse.itk.org/u/mark_john)\
**Replies:** 2\
**Last updated:** [December 4, 2018, 2:13pm UTC](https://discourse.itk.org/t/how-to-convert-a-anisotropic-to-isotropic-and-then-back-to-anisotropic/1451 "2018-12-04T14:13:27Z")

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Hello, I have a reference image that is isotropic (1mm x 1mm x 1mm). A target image is anisotropic (0.5 mm x0.5mmx2mm). I want to convert the target image to isotropic that same with the reference image. After obtaining …

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## [Best practices for initialization before optimizer-based 2D registration](https://discourse.itk.org/t/best-practices-for-initialization-before-optimizer-based-2d-registration/1433)

<div class="topic-metadata">

**Author:** [@take5v](https://discourse.itk.org/u/take5v)\
**Replies:** 2\
**Last updated:** [November 27, 2018, 3:51pm UTC](https://discourse.itk.org/t/best-practices-for-initialization-before-optimizer-based-2d-registration/1433 "2018-11-27T15:51:55Z")

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Hi, Since optimizer-based registration is performed in physical coordinates it is crucial to setup coarse initial transformation. For some medical images, this transformation could be calculated with image origin, spac…

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## [writing .png image not working](https://discourse.itk.org/t/writing-png-image-not-working/1431)

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**Author:** [@hothao](https://discourse.itk.org/u/hothao)\
**Replies:** 1\
**Last updated:** [November 21, 2018, 2:58pm UTC](https://discourse.itk.org/t/writing-png-image-not-working/1431 "2018-11-21T14:58:34Z")

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Hi everyone! I’m trying to write Cannyfilter image as a .png image. It has no bugs. But it does not work. Here is the message: itk::ExceptionObject (000000926B4FD6A0) Location: "void \_\_cdecl itk::PNGImageIO::WriteSlic…

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## [Numpy bridge with image vectors](https://discourse.itk.org/t/numpy-bridge-with-image-vectors/1422)

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**Author:** [@simon.rit](https://discourse.itk.org/u/simon.rit)\
**Replies:** 2\
**Last updated:** [November 20, 2018, 10:42am UTC](https://discourse.itk.org/t/numpy-bridge-with-image-vectors/1422 "2018-11-20T10:42:20Z")

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Hi, It seems to me that the numpy bridge does not work for “itk::Image\<itk::Vector” types. For example, if I (manually) run the test test\_NumPyBridge\_itkVectorPixelImage, the convertedvectorImage is not of the same typ…

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## [Why ResampleImageFilter is slow?](https://discourse.itk.org/t/why-resampleimagefilter-is-slow/1217)

<div class="topic-metadata">

**Author:** [@denis.p.shamonin](https://discourse.itk.org/u/denis.p.shamonin)\
**Replies:** 46\
**Last updated:** [October 25, 2018, 12:25pm UTC](https://discourse.itk.org/t/why-resampleimagefilter-is-slow/1217 "2018-10-25T12:25:29Z")

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Dear developers, I’ve notices strange performance drop in ResampleImageFilter. Here is my logs from ITK 4.12.2, 25 Oct 2017 on the same machine same compiler etc. ITK 4.12.2 ResampleImageFilter ; 3 ; 512x512x256 ; 79…

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## [Difference between Rigid3DTransform Euler3DTransform](https://discourse.itk.org/t/difference-between-rigid3dtransform-euler3dtransform/1339)

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**Author:** [@ibr](https://discourse.itk.org/u/ibr)\
**Replies:** 4\
**Last updated:** [October 9, 2018, 7:26am UTC](https://discourse.itk.org/t/difference-between-rigid3dtransform-euler3dtransform/1339 "2018-10-09T07:26:41Z")

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Rigid3DTransform and Euler3DTransform It is not clear, I appreciate if someone explains the difference. Another question can someone check my computation bellow is correct: import numpy as np import sys, math print("…

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## [Python Environment](https://discourse.itk.org/t/python-environment/1336)

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**Author:** [@melrobin](https://discourse.itk.org/u/melrobin)\
**Replies:** 6\
**Last updated:** [October 8, 2018, 6:53pm UTC](https://discourse.itk.org/t/python-environment/1336 "2018-10-08T18:53:10Z")

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I am having trouble getting my Python environment set up and I know that I have screwed something up. I am building from sources and install to the system site-packages directory. The install stores many ITK related .p…

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## [MacOS 10.14 SDK](https://discourse.itk.org/t/macos-10-14-sdk/1295)

<div class="topic-metadata">

**Author:** [@spinicist](https://discourse.itk.org/u/spinicist)\
**Replies:** 4\
**Last updated:** [September 20, 2018, 7:35pm UTC](https://discourse.itk.org/t/macos-10-14-sdk/1295 "2018-09-20T19:35:31Z")

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Hi, Sorry, this isn’t specifically an ITK issue (I think), but I’m struggling to think where else to ask for help. I compile my tools that use ITK on a Mac. Last night, my Mac appears to have downloaded an XCode update…

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## [Visual Studio VS 2017 15.8.0: Internal compiler error with NumericTraits](https://discourse.itk.org/t/visual-studio-vs-2017-15-8-0-internal-compiler-error-with-numerictraits/1205)

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**Author:** [@Sophonet](https://discourse.itk.org/u/Sophonet)\
**Replies:** 7\
**Last updated:** [September 12, 2018, 3:29pm UTC](https://discourse.itk.org/t/visual-studio-vs-2017-15-8-0-internal-compiler-error-with-numerictraits/1205 "2018-09-12T15:29:10Z")

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Just for your information: I have filed a bug report here https://developercommunity.visualstudio.com/content/problem/312703/vs-1580-internal-compiler-error.html - since itk’s NumericTraits::max() seem to cause a problem…

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## [ITKVTKglue failing](https://discourse.itk.org/t/itkvtkglue-failing/1223)

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**Author:** [@Rhodri\_Smith](https://discourse.itk.org/u/Rhodri_Smith)\
**Replies:** 7\
**Last updated:** [August 23, 2018, 5:28pm UTC](https://discourse.itk.org/t/itkvtkglue-failing/1223 "2018-08-23T17:28:23Z")

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Hi I get this error when ticking the flag for ITKVTKglue when building ITK: /vcl\_compiler.h:243:0, CMakeFiles/Makefile2:34960: recipe for target ‘Modules/Bridge/VtkGlue/src/CMakeFiles/ITKVtkGlue.dir/all’ failed Lots o…

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## [RecursiveSeparableImageFilter the normal execution flow is broken.](https://discourse.itk.org/t/recursiveseparableimagefilter-the-normal-execution-flow-is-broken/1216)

<div class="topic-metadata">

**Author:** [@denis.p.shamonin](https://discourse.itk.org/u/denis.p.shamonin)\
**Replies:** 3\
**Last updated:** [August 22, 2018, 3:20pm UTC](https://discourse.itk.org/t/recursiveseparableimagefilter-the-normal-execution-flow-is-broken/1216 "2018-08-22T15:20:37Z")

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Dear Dženan Zukić, Recently you have changed the RecursiveSeparableImageFilter for new threading support. Change-Id: I5ce9d8b965035c9716ee5b25694d39bc15ba666e Date: Wed Aug 1 12:45:38 2018 -0400 ENH: refactoring Re…

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## [Bug in itkHistogram.hxx leading to an endless loop](https://discourse.itk.org/t/bug-in-itkhistogram-hxx-leading-to-an-endless-loop/1190)

<div class="topic-metadata">

**Author:** [@madsdk](https://discourse.itk.org/u/madsdk)\
**Replies:** 4\
**Last updated:** [August 16, 2018, 2:23pm UTC](https://discourse.itk.org/t/bug-in-itkhistogram-hxx-leading-to-an-endless-loop/1190 "2018-08-16T14:23:15Z")

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Hello, I have identified a bug in the binary search in itkHistogram.hxx that make a loop run forever. The lines in question are these: // Binary search for the bin where this measurement could be mid = ( end + 1 ) / 2;…

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## [ITK 4.13.0 Python wrapping does not compile with VS 2017 15.7.4 with V14.14 tools](https://discourse.itk.org/t/itk-4-13-0-python-wrapping-does-not-compile-with-vs-2017-15-7-4-with-v14-14-tools/1052)

<div class="topic-metadata">

**Author:** [@Sophonet](https://discourse.itk.org/u/Sophonet)\
**Replies:** 6\
**Last updated:** [August 13, 2018, 2:48pm UTC](https://discourse.itk.org/t/itk-4-13-0-python-wrapping-does-not-compile-with-vs-2017-15-7-4-with-v14-14-tools/1052 "2018-08-13T14:48:06Z")

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Hi - after having upgraded VS 2017 to 15.7.4 a few days ago, ITK 4.13.0 with Python wrapping does not compile anymore - there are tons of errors pointing to syntactic errors in MSVC/14.14.26428/include/… It seems that th…

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