# Beginner Questions

**URL:** https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=36

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**Page:** 37

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## [erosion does not erode the image. It returns the same binary image as the input](https://discourse.itk.org/t/erosion-does-not-erode-the-image-it-returns-the-same-binary-image-as-the-input/1901)

<div class="topic-metadata">

**Author:** [@zandarina](https://discourse.itk.org/u/zandarina)\
**Replies:** 6\
**Last updated:** [May 21, 2019, 3:59pm UTC](https://discourse.itk.org/t/erosion-does-not-erode-the-image-it-returns-the-same-binary-image-as-the-input/1901 "2019-05-21T15:59:11Z")

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Hi I am writing because i am trying to erode the image obtained after a threshold to avoid the leakage between 2 objects. Like the example of two coins merged in one and the erosion splits them into two coins. But my p…

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## ["No imageIO registered" - error message in python ITK](https://discourse.itk.org/t/no-imageio-registered-error-message-in-python-itk/1894)

<div class="topic-metadata">

**Author:** [@EE18D504\_SINDHURA\_C](https://discourse.itk.org/u/EE18D504_SINDHURA_C)\
**Replies:** 1\
**Last updated:** [May 21, 2019, 4:31am UTC](https://discourse.itk.org/t/no-imageio-registered-error-message-in-python-itk/1894 "2019-05-21T04:31:49Z")

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I just tried using ITK Python from the link below I installed all requirements and i tried simulating the following code import itkConfig import itkExtras itkConfig.ProgressCallback = itkExtras.simple\_progress\_cal…

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## [Default BackgroundValue in erode/dilate filters](https://discourse.itk.org/t/default-backgroundvalue-in-erode-dilate-filters/1876)

<div class="topic-metadata">

**Author:** [@alkamid](https://discourse.itk.org/u/alkamid)\
**Replies:** 3\
**Last updated:** [May 21, 2019, 4:08am UTC](https://discourse.itk.org/t/default-backgroundvalue-in-erode-dilate-filters/1876 "2019-05-21T04:08:04Z")

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I am trying to erode a binary image using the Pythonic interface (using ITK 5.0 rc2). From BinaryErodeImageFilter’s documentation: The eroded pixels will receive the BackgroundValue (defaults to 0). This doesn’t see…

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## [ITK with DCMTK building error](https://discourse.itk.org/t/itk-with-dcmtk-building-error/593)

<div class="topic-metadata">

**Author:** [@tim-evain](https://discourse.itk.org/u/tim-evain)\
**Replies:** 26\
**Last updated:** [May 16, 2019, 9:00am UTC](https://discourse.itk.org/t/itk-with-dcmtk-building-error/593 "2019-05-16T09:00:38Z")

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Hi everyone, I’m currently trying to build the latest release with DCMTK+ICU. Compilation fails due to the following error: \[…\]/ITK\_4-13/Modules/ThirdParty/DCMTK/ITKDCMTK\_ExtProject/ofstd/libsrc/ofchrenc.cc:58:10: fat…

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## [\[fixed\]How to read raw data using simpleitk?](https://discourse.itk.org/t/fixed-how-to-read-raw-data-using-simpleitk/1858)

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**Author:** [@hubutui](https://discourse.itk.org/u/hubutui)\
**Replies:** 2\
**Last updated:** [May 15, 2019, 8:32am UTC](https://discourse.itk.org/t/fixed-how-to-read-raw-data-using-simpleitk/1858 "2019-05-15T08:32:03Z")

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Hi, I’m trying to read an image without meta header. I’m told that I could use ImageJ/Fiji to open the image by “File menu \> import \> Raw”, and set Image type: 16-bit Unsigned Width: 2048 pixels Height: 2048 pixels …

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## [ImageFileWriter crashes when writing MHD file to long absolute path](https://discourse.itk.org/t/imagefilewriter-crashes-when-writing-mhd-file-to-long-absolute-path/1856)

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**Author:** [@lukas](https://discourse.itk.org/u/lukas)\
**Replies:** 7\
**Last updated:** [May 14, 2019, 10:00am UTC](https://discourse.itk.org/t/imagefilewriter-crashes-when-writing-mhd-file-to-long-absolute-path/1856 "2019-05-14T10:00:58Z")

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Hi all, I have encountered a problem with the itk::ImageFileWriter when writing mhd files. When the absolute path exceeds 263 characters, the program crashes with a segfault in the UnRegister method of the itkSmartPoin…

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## [Affine registration in itk](https://discourse.itk.org/t/affine-registration-in-itk/1868)

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**Author:** [@c.spanakis83](https://discourse.itk.org/u/c.spanakis83)\
**Replies:** 1\
**Last updated:** [May 13, 2019, 1:32pm UTC](https://discourse.itk.org/t/affine-registration-in-itk/1868 "2019-05-13T13:32:24Z")

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Hello. I want to experiment with affine registration in ITK. In the itk::AffineTransform\< TParametersValueType, NDimensions \> Class Template, it is possible to specify the rotation center (which, by default, is the origi…

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## [Python filter example](https://discourse.itk.org/t/python-filter-example/1853)

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**Author:** [@finetjul](https://discourse.itk.org/u/finetjul)\
**Replies:** 3\
**Last updated:** [May 9, 2019, 3:44pm UTC](https://discourse.itk.org/t/python-filter-example/1853 "2019-05-09T15:44:15Z")

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Hi, I would like to write an ITK filter in Python. Is there an example somewhere ? Thanks, Julien.

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## [SimpleITK memory access violation when using large images.](https://discourse.itk.org/t/simpleitk-memory-access-violation-when-using-large-images/1845)

<div class="topic-metadata">

**Author:** [@mattias](https://discourse.itk.org/u/mattias)\
**Replies:** 12\
**Last updated:** [May 9, 2019, 1:51pm UTC](https://discourse.itk.org/t/simpleitk-memory-access-violation-when-using-large-images/1845 "2019-05-09T13:51:50Z")

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Not really sure if this is a beginner question, but at least it’s my first question. I’m having problems when using newer versions of SimpleITK with relatively large images (500M+ voxels), it causes memory access violati…

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## [How to disable particular default module](https://discourse.itk.org/t/how-to-disable-particular-default-module/1840)

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**Author:** [@mihail.isakov](https://discourse.itk.org/u/mihail.isakov)\
**Replies:** 7\
**Last updated:** [May 8, 2019, 1:35pm UTC](https://discourse.itk.org/t/how-to-disable-particular-default-module/1840 "2019-05-08T13:35:44Z")

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Hello, I would like disable some default modules, specially GDCM / GDCMIO, in my application i use own stuff for DICOM and also GDCM-clone library, so i don’t need the module. Is it possible with some command line argu…

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## [Patients ID in DICOM in the USA](https://discourse.itk.org/t/patients-id-in-dicom-in-the-usa/1843)

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**Author:** [@hadasara](https://discourse.itk.org/u/hadasara)\
**Replies:** 2\
**Last updated:** [May 6, 2019, 10:47pm UTC](https://discourse.itk.org/t/patients-id-in-dicom-in-the-usa/1843 "2019-05-06T22:47:17Z")

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Hi all, As a non-USA citizen I was wondering what is wriiten as a patient ID in the DICOM tags. Is it passport number? Is it internal ID of hospital system? Is it something else? Thanks!

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## [Get the metadata of dicom without reading the image](https://discourse.itk.org/t/get-the-metadata-of-dicom-without-reading-the-image/1833)

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**Author:** [@zandarina](https://discourse.itk.org/u/zandarina)\
**Replies:** 2\
**Last updated:** [May 6, 2019, 8:34am UTC](https://discourse.itk.org/t/get-the-metadata-of-dicom-without-reading-the-image/1833 "2019-05-06T08:34:37Z")

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Dear all, I would like to get the windows level and the windows width but without reading the image. I read in this forum that this is possible but i did not find any example without updating the reader. My code works w…

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## [How does the Image Registration or Image Alignment work on the pixel level?](https://discourse.itk.org/t/how-does-the-image-registration-or-image-alignment-work-on-the-pixel-level/1826)

<div class="topic-metadata">

**Author:** [@Akshay\_Kulkarni](https://discourse.itk.org/u/Akshay_Kulkarni)\
**Replies:** 5\
**Last updated:** [May 2, 2019, 6:14am UTC](https://discourse.itk.org/t/how-does-the-image-registration-or-image-alignment-work-on-the-pixel-level/1826 "2019-05-02T06:14:14Z")

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I know the basic flow or process of the Image Registration/Alignment but what happens at the pixel level when 2 images are registered/aligned i.e. similar pixels of moving image which are transformed to the fixed image a…

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## [\[fixed\]Is hausdorff distance implement in SimpleITK aware of spacing?](https://discourse.itk.org/t/fixed-is-hausdorff-distance-implement-in-simpleitk-aware-of-spacing/1830)

<div class="topic-metadata">

**Author:** [@hubutui](https://discourse.itk.org/u/hubutui)\
**Replies:** 1\
**Last updated:** [May 1, 2019, 3:12pm UTC](https://discourse.itk.org/t/fixed-is-hausdorff-distance-implement-in-simpleitk-aware-of-spacing/1830 "2019-05-01T15:12:14Z")

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I check https://itk.org/SimpleITKDoxygen/html/classitk\_1\_1simple\_1\_1HausdorffDistanceImageFilter.html, but still confused. Is hausdorff distance implement in SimpleITK aware of spacing? Does the HausdorffDistanceImageF…

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## [Install ITK library into Xcode 10](https://discourse.itk.org/t/install-itk-library-into-xcode-10/1821)

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**Author:** [@yinpeter](https://discourse.itk.org/u/yinpeter)\
**Replies:** 1\
**Last updated:** [April 30, 2019, 7:51pm UTC](https://discourse.itk.org/t/install-itk-library-into-xcode-10/1821 "2019-04-30T19:51:36Z")

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I am new in ITK and have read “The ITK Software Guide”, but I can not find the solution of build/compile/install the static/shared library into Mac Xcode 10, please help me to do this, thanks a lot!

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## [Why are empty spaces observed after performing Deformable registration ?](https://discourse.itk.org/t/why-are-empty-spaces-observed-after-performing-deformable-registration/1810)

<div class="topic-metadata">

**Author:** [@EE18D504\_SINDHURA\_C](https://discourse.itk.org/u/EE18D504_SINDHURA_C)\
**Replies:** 1\
**Last updated:** [April 29, 2019, 4:23pm UTC](https://discourse.itk.org/t/why-are-empty-spaces-observed-after-performing-deformable-registration/1810 "2019-04-29T16:23:26Z")

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I am trying to register two CT scans of the brain. I have used B-spline transformation code. The output I get after the registration is having some spaces as shown below. How to deal with it? How to apply the inverse tra…

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## [how to use ITK in my own project in visual studio](https://discourse.itk.org/t/how-to-use-itk-in-my-own-project-in-visual-studio/1805)

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**Author:** [@maioda](https://discourse.itk.org/u/maioda)\
**Replies:** 2\
**Last updated:** [April 26, 2019, 6:32pm UTC](https://discourse.itk.org/t/how-to-use-itk-in-my-own-project-in-visual-studio/1805 "2019-04-26T18:32:35Z")

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hi , i’m new in ITK trying to include ITK in my own project in visual studio 2017 by doing : 1-project-\>properties-\>c/c+±\>general-\>Additional Include 2-project-\>properties-\>Linker-\>general-\>Additional Library 3–proj…

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## [import 3D volume from itk to vtk](https://discourse.itk.org/t/import-3d-volume-from-itk-to-vtk/1673)

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**Author:** [@Marco\_Festugato](https://discourse.itk.org/u/Marco_Festugato)\
**Replies:** 7\
**Last updated:** [April 26, 2019, 6:30pm UTC](https://discourse.itk.org/t/import-3d-volume-from-itk-to-vtk/1673 "2019-04-26T18:30:55Z")

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Hi guys! I’ve managed to read 200 DICOM files and use them to compose a volume…how can i pass this volume to VTK in order to actually see it? Thank u all for your answer :slight\_smile:

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## [MattesMutualInformationImageToImageMetricv4 - Getting the rotation result](https://discourse.itk.org/t/mattesmutualinformationimagetoimagemetricv4-getting-the-rotation-result/1793)

<div class="topic-metadata">

**Author:** [@OmerB](https://discourse.itk.org/u/OmerB)\
**Replies:** 2\
**Last updated:** [April 17, 2019, 2:12pm UTC](https://discourse.itk.org/t/mattesmutualinformationimagetoimagemetricv4-getting-the-rotation-result/1793 "2019-04-17T14:12:23Z")

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Hello everyone, I have been using ITK for image registration. Currently, I am looking to improve the accuracy the registration, and therefore trying to upgrade to ITKV4. My current implementation of ITKV3 is using Mat…

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## [ITK Modules a comprehensive list](https://discourse.itk.org/t/itk-modules-a-comprehensive-list/1701)

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**Author:** [@pip010](https://discourse.itk.org/u/pip010)\
**Replies:** 4\
**Last updated:** [April 17, 2019, 9:31am UTC](https://discourse.itk.org/t/itk-modules-a-comprehensive-list/1701 "2019-04-17T09:31:48Z")

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When using ITK modules binding in cmake based on : find\_package(ITK REQUIRED COMPONENTS ITKCommon etc. ) how do I determine which header in which module/component it belongs to? Where is a comprehensive list of all …

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## [Writing filter with multiple outputs - do I need to provide the number of outputs already in the constructor?](https://discourse.itk.org/t/writing-filter-with-multiple-outputs-do-i-need-to-provide-the-number-of-outputs-already-in-the-constructor/1781)

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**Author:** [@hellman](https://discourse.itk.org/u/hellman)\
**Replies:** 1\
**Last updated:** [April 12, 2019, 2:15pm UTC](https://discourse.itk.org/t/writing-filter-with-multiple-outputs-do-i-need-to-provide-the-number-of-outputs-already-in-the-constructor/1781 "2019-04-12T14:15:52Z")

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Hi, I am writing my own ImageSource derived filter that I’d like to output multiple images. The number of outputs, however, is not known already in the constructor, but is a parameter that can be set by a Setter-functio…

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## [How to control iteration step by step in levelset-based filter?](https://discourse.itk.org/t/how-to-control-iteration-step-by-step-in-levelset-based-filter/1761)

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**Author:** [@wenyalin](https://discourse.itk.org/u/wenyalin)\
**Replies:** 1\
**Last updated:** [April 9, 2019, 1:15pm UTC](https://discourse.itk.org/t/how-to-control-iteration-step-by-step-in-levelset-based-filter/1761 "2019-04-09T13:15:47Z")

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Hey guys, I’m a newbie in ITK. I’m wondering how could the GAC Level Set example achieve animated display? (link below, “Results” section) https://itk.org/ITKExamples/src/Segmentation/LevelSets/SegmentWithGeodesicActiv…

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## [ITK Take Too Long To read Double type image](https://discourse.itk.org/t/itk-take-too-long-to-read-double-type-image/917)

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**Author:** [@wyBrian](https://discourse.itk.org/u/wyBrian)\
**Replies:** 12\
**Last updated:** [April 8, 2019, 1:12pm UTC](https://discourse.itk.org/t/itk-take-too-long-to-read-double-type-image/917 "2019-04-08T13:12:37Z")

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Hi, all: Lately, I am coding an python app using itk. For dcm files IO, i try itk.ImageFileReader and itk.ImageSeriesReader, both take too long to read dcm with double type image. Environment is homebrewed ITK on Mac. L…

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## [Specifying ImageIO when reading a file in Python](https://discourse.itk.org/t/specifying-imageio-when-reading-a-file-in-python/1754)

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**Author:** [@alkamid](https://discourse.itk.org/u/alkamid)\
**Replies:** 2\
**Last updated:** [April 8, 2019, 7:07am UTC](https://discourse.itk.org/t/specifying-imageio-when-reading-a-file-in-python/1754 "2019-04-08T07:07:50Z")

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With SimpleITK, I can specify ImageIO when reading a file: image = sitk.ReadImage(filename, sitk.sitkInt16, 'GiplImageIO') Is there a similar, Pythonic interface for this in itk-5.0rc1? I tried: img = itk.image\_file\_r…

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## [AdaptiveHistogramEqualizationImageFilter- parameter tuning](https://discourse.itk.org/t/adaptivehistogramequalizationimagefilter-parameter-tuning/1738)

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**Author:** [@Courtney\_Ambrozic](https://discourse.itk.org/u/Courtney_Ambrozic)\
**Replies:** 2\
**Last updated:** [April 3, 2019, 4:46pm UTC](https://discourse.itk.org/t/adaptivehistogramequalizationimagefilter-parameter-tuning/1738 "2019-04-03T16:46:14Z")

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Hello, Regarding the AdaptiveHistogramEqualizationImageFilter, is there a way to set the function to completely behave as a classical histogram equalization method? Once alpha is set to 0, does beta represent a range f…

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## [m\_UseSequentialSampling error while performing registration of two 3D images of same modality](https://discourse.itk.org/t/m-usesequentialsampling-error-while-performing-registration-of-two-3d-images-of-same-modality/1728)

<div class="topic-metadata">

**Author:** [@EE18D504\_SINDHURA\_C](https://discourse.itk.org/u/EE18D504_SINDHURA_C)\
**Replies:** 6\
**Last updated:** [April 2, 2019, 5:48pm UTC](https://discourse.itk.org/t/m-usesequentialsampling-error-while-performing-registration-of-two-3d-images-of-same-modality/1728 "2019-04-02T17:48:43Z")

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I am trying to execute the code from following page for my registration I removed all this exception handling code …as I am not much aware of it. and tried executing. the error comes while executing registration-\>upda…

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## [Building and integrating external modules](https://discourse.itk.org/t/building-and-integrating-external-modules/884)

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**Author:** [@Gordian](https://discourse.itk.org/u/Gordian)\
**Replies:** 9\
**Last updated:** [September 26, 2018, 8:10pm UTC](https://discourse.itk.org/t/building-and-integrating-external-modules/884 "2018-09-26T20:10:38Z")

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Hello again, I want to use an external module e.g. itkOBBLabelMap. My approach to buidl ITK with the external module: The following is a brief list of instructions to get a external module into ITK: cd ITK/Modules/…

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## [How to apply a .vtk file as mask to my 3d Image](https://discourse.itk.org/t/how-to-apply-a-vtk-file-as-mask-to-my-3d-image/1717)

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**Author:** [@siaeleni](https://discourse.itk.org/u/siaeleni)\
**Replies:** 1\
**Last updated:** [March 29, 2019, 1:45pm UTC](https://discourse.itk.org/t/how-to-apply-a-vtk-file-as-mask-to-my-3d-image/1717 "2019-03-29T13:45:09Z")

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Hello, I have a .vtk model that I have created and I want to apply that as a mask to my 3d Image. Do you have any idea how can I approach that? Thanks, Eleni

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## [Adaptive Histogram Equalization for 3D images- long run-time](https://discourse.itk.org/t/adaptive-histogram-equalization-for-3d-images-long-run-time/1705)

<div class="topic-metadata">

**Author:** [@Courtney\_Ambrozic](https://discourse.itk.org/u/Courtney_Ambrozic)\
**Replies:** 4\
**Last updated:** [March 26, 2019, 3:56pm UTC](https://discourse.itk.org/t/adaptive-histogram-equalization-for-3d-images-long-run-time/1705 "2019-03-26T15:56:57Z")

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Hello, I’m running the AdaptiveHistogramEqualizationImageFilter() on a 3D image that is 512x512x197. Currently, the run-time for this histogram equalization is about three hours. Does anyone have an idea as to why it …

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## [Calculating Eigenvectors using Python and ITK](https://discourse.itk.org/t/calculating-eigenvectors-using-python-and-itk/1638)

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**Author:** [@vero](https://discourse.itk.org/u/vero)\
**Replies:** 2\
**Last updated:** [March 22, 2019, 8:50am UTC](https://discourse.itk.org/t/calculating-eigenvectors-using-python-and-itk/1638 "2019-03-22T08:50:09Z")

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Hey, I’m trying to calculate eigenvalues and -vectors of a hessian matrix I received with the HessianRecursiveGaussianImageFilter using Python. So far I found neither in SimpleITK nor in ITK an algorithm that would work…

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