# Uncategorized

**URL:** https://discourse.itk.org/c/uncategorized/1.md?no_subcategories=false&page=12

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

**Page:** 13

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## [Histogram Fixed Bin Size](https://discourse.itk.org/t/histogram-fixed-bin-size/2243)

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**Author:** [@sarthakpati](https://discourse.itk.org/u/sarthakpati)\
**Replies:** 1\
**Last updated:** [September 11, 2019, 8:30pm UTC](https://discourse.itk.org/t/histogram-fixed-bin-size/2243 "2019-09-11T20:30:27Z")

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Hi, I am trying to calculated Histogram based on the Fixed Bin Size (as opposed to giving the number of total bins). Is that possible in ITK? Reference: https://ibsi.readthedocs.io/en/latest/03\_Image\_processing.html?hi…

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## [concatenating dense deformation fields](https://discourse.itk.org/t/concatenating-dense-deformation-fields/2238)

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**Author:** [@sedghi](https://discourse.itk.org/u/sedghi)\
**Replies:** 10\
**Last updated:** [September 11, 2019, 1:42pm UTC](https://discourse.itk.org/t/concatenating-dense-deformation-fields/2238 "2019-09-11T13:42:28Z")

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I was wondering if it is possible to concatenate two dense deformation fields in ITK python or SimpleITK. Having B = T2 ( T1 ( A(x) ) ) In which T1, and T2 are both dense deformation fields (both with size ofImage …

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## [FastMarchingSegmentation Graphical Interface?](https://discourse.itk.org/t/fastmarchingsegmentation-graphical-interface/2225)

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**Author:** [@ral\_san](https://discourse.itk.org/u/ral_san)\
**Replies:** 5\
**Last updated:** [September 5, 2019, 5:19pm UTC](https://discourse.itk.org/t/fastmarchingsegmentation-graphical-interface/2225 "2019-09-05T17:19:23Z")

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Hi Guys, I want to apply the FastMarchingSegmentation Filter. In the documentation https://simpleitk.readthedocs.io/en/master/Examples/FastMarchingSegmentation/Documentation.html is mentioned that it’s possible to view…

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## [ITK error : GDCM could not read the DICOM image showing “DicomImageReadWrite.exe has triggered a breakpoint.” error while debugging.](https://discourse.itk.org/t/itk-error-gdcm-could-not-read-the-dicom-image-showing-dicomimagereadwrite-exe-has-triggered-a-breakpoint-error-while-debugging/2155)

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**Author:** [@Pooja\_Virkar](https://discourse.itk.org/u/Pooja_Virkar)\
**Replies:** 19\
**Last updated:** [August 29, 2019, 2:55pm UTC](https://discourse.itk.org/t/itk-error-gdcm-could-not-read-the-dicom-image-showing-dicomimagereadwrite-exe-has-triggered-a-breakpoint-error-while-debugging/2155 "2019-08-29T14:55:17Z")

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Hello, I am trying to run DicomImageReadWrite.cxxx example from ITK website in Visual Studio 2019. I have my input dicom image in working directory and gave correct command arguments in Properties. But still while run…

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## [Transforms not working as expected](https://discourse.itk.org/t/transforms-not-working-as-expected/2192)

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**Author:** [@kekday](https://discourse.itk.org/u/kekday)\
**Replies:** 1\
**Last updated:** [August 27, 2019, 7:42pm UTC](https://discourse.itk.org/t/transforms-not-working-as-expected/2192 "2019-08-27T19:42:10Z")

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Do transforms in SimpleITK work differently than the conventional representations? In SITK, if I understand correctly, the usual transformation matrix is broken down into the translation part and the “matrix” part. For i…

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## [Registration Initialization](https://discourse.itk.org/t/registration-initialization/2164)

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**Author:** [@kekday](https://discourse.itk.org/u/kekday)\
**Replies:** 1\
**Last updated:** [August 19, 2019, 1:06pm UTC](https://discourse.itk.org/t/registration-initialization/2164 "2019-08-19T13:06:28Z")

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Hi all, I am very new to ITK and I was looking at this notebook More specifically I see the initialization was done using initial\_transform = sitk.CenteredTransformInitializer(fixed\_image, moving\_image, sitk.Euler3…

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## [Slope and intercept when reading Nifti images](https://discourse.itk.org/t/slope-and-intercept-when-reading-nifti-images/2122)

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**Author:** [@Elli](https://discourse.itk.org/u/Elli)\
**Replies:** 8\
**Last updated:** [August 15, 2019, 2:38pm UTC](https://discourse.itk.org/t/slope-and-intercept-when-reading-nifti-images/2122 "2019-08-15T14:38:43Z")

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Dear all, I have a very basic question: I am reading in nifti images using: ImageType::Pointer readImage(string imageName) { typename ReaderType::Pointer reader = ReaderType::New(); reader-\>SetFileName(imageName); t…

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## [is it possible to write/save to disk all the meta-data of a DICOM image without explicitly stating which tags to copy?](https://discourse.itk.org/t/is-it-possible-to-write-save-to-disk-all-the-meta-data-of-a-dicom-image-without-explicitly-stating-which-tags-to-copy/2125)

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**Author:** [@ral\_san](https://discourse.itk.org/u/ral_san)\
**Replies:** 6\
**Last updated:** [August 14, 2019, 3:10pm UTC](https://discourse.itk.org/t/is-it-possible-to-write-save-to-disk-all-the-meta-data-of-a-dicom-image-without-explicitly-stating-which-tags-to-copy/2125 "2019-08-14T15:10:15Z")

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I am resampling a DICOM CT image and after resampling I would like to save it to disk as new image. I found this example https://simpleitk.readthedocs.io/en/master/Examples/DicomSeriesReadModifyWrite/Documentation.html …

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## [Free memory and delete links of VTKSmartPointer Polydata](https://discourse.itk.org/t/free-memory-and-delete-links-of-vtksmartpointer-polydata/2130)

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**Author:** [@srbn.ghosh89](https://discourse.itk.org/u/srbn.ghosh89)\
**Replies:** 2\
**Last updated:** [August 7, 2019, 9:34pm UTC](https://discourse.itk.org/t/free-memory-and-delete-links-of-vtksmartpointer-polydata/2130 "2019-08-07T21:34:01Z")

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Hi, In my mesh, there are 642473 cells and 1275549 points. I want to replace cell of the mesh and after replacement, I want to reassign the mesh on the same name. But before reassign how can I free the memory and del…

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## [Retrospective Image Registration Evaluation - service not working for me](https://discourse.itk.org/t/retrospective-image-registration-evaluation-service-not-working-for-me/2093)

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**Author:** [@Peter.Roesch](https://discourse.itk.org/u/Peter.Roesch)\
**Replies:** 3\
**Last updated:** [August 5, 2019, 10:11am UTC](https://discourse.itk.org/t/retrospective-image-registration-evaluation-service-not-working-for-me/2093 "2019-08-05T10:11:41Z")

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Hello, I would like to evaluate the accuracy of a registration approach using https://www.insight-journal.org/rire There were no error messages when I submitted transformations according to the guidelines. However, if …

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## [How to detect the edge of very noisy image?](https://discourse.itk.org/t/how-to-detect-the-edge-of-very-noisy-image/2090)

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**Author:** [@srbn.ghosh89](https://discourse.itk.org/u/srbn.ghosh89)\
**Replies:** 6\
**Last updated:** [July 27, 2019, 1:09pm UTC](https://discourse.itk.org/t/how-to-detect-the-edge-of-very-noisy-image/2090 "2019-07-27T13:09:50Z")

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I have this image of a cell which is very noisy and the edge of the circle cannot be detected. Which filter can be used to get the edge?

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## [Calculate the centroid of a simplex surface?](https://discourse.itk.org/t/calculate-the-centroid-of-a-simplex-surface/2096)

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**Author:** [@srbn.ghosh89](https://discourse.itk.org/u/srbn.ghosh89)\
**Replies:** 3\
**Last updated:** [July 26, 2019, 8:55pm UTC](https://discourse.itk.org/t/calculate-the-centroid-of-a-simplex-surface/2096 "2019-07-26T20:55:53Z")

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I have simplex surface and I need to calculate centroid of different parts of the simplex? The edges are not similar in every side. Screenshots attached.

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## [How to segment the thin skin edge of body parts?](https://discourse.itk.org/t/how-to-segment-the-thin-skin-edge-of-body-parts/2078)

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**Author:** [@srbn.ghosh89](https://discourse.itk.org/u/srbn.ghosh89)\
**Replies:** 16\
**Last updated:** [July 26, 2019, 2:29pm UTC](https://discourse.itk.org/t/how-to-segment-the-thin-skin-edge-of-body-parts/2078 "2019-07-26T14:29:51Z")

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I have 3D image slices of chest. I only want to get the outer skin surface of the chest which will exclude all the organs inside. What kind of segmentation can be applied to get only the skin surface?

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## [build error with ITK5 SpatialObjects scene](https://discourse.itk.org/t/build-error-with-itk5-spatialobjects-scene/2062)

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**Author:** [@pieper](https://discourse.itk.org/u/pieper)\
**Replies:** 7\
**Last updated:** [July 22, 2019, 6:27pm UTC](https://discourse.itk.org/t/build-error-with-itk5-spatialobjects-scene/2062 "2019-07-22T18:27:03Z")

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Hi - I tried building Slicer against ITK’s v5.0.0 tag and got the errors below. The normal slicer builds use an 5.0-rc1 so something must have snuck in at the end. Can anyone suggest a fix or point me to a porting doc…

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## [Append 2 volumes change in resolution?](https://discourse.itk.org/t/append-2-volumes-change-in-resolution/2036)

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**Author:** [@srbn.ghosh89](https://discourse.itk.org/u/srbn.ghosh89)\
**Replies:** 4\
**Last updated:** [July 15, 2019, 8:02pm UTC](https://discourse.itk.org/t/append-2-volumes-change-in-resolution/2036 "2019-07-15T20:02:59Z")

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I am trying to Append 2 volumes. But thereafter I can see that the resolution has changed a lot. Why did this happen? These pictures are before and after.

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## [Use of Mask Image filter in liver segmentation](https://discourse.itk.org/t/use-of-mask-image-filter-in-liver-segmentation/1990)

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**Author:** [@Pooja\_Virkar](https://discourse.itk.org/u/Pooja_Virkar)\
**Replies:** 4\
**Last updated:** [July 1, 2019, 1:57pm UTC](https://discourse.itk.org/t/use-of-mask-image-filter-in-liver-segmentation/1990 "2019-07-01T13:57:39Z")

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Hello, I would like to segment the liver. I used different algorithms in 3D data. But i am unable to get exact liver part in my output. Other regions are also coming. I tried using “maskImagefilter”. but I am getting …

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## [Trimming down ITK build to just used parts](https://discourse.itk.org/t/trimming-down-itk-build-to-just-used-parts/1995)

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**Author:** [@gdevenyi](https://discourse.itk.org/u/gdevenyi)\
**Replies:** 4\
**Last updated:** [June 26, 2019, 6:04pm UTC](https://discourse.itk.org/t/trimming-down-itk-build-to-just-used-parts/1995 "2019-06-26T18:04:14Z")

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I’m investigating trimming down the ANTs superbuild to include the minimum components of ITK/VTK required for it to function. I was wondering, can anyone suggest a method to determine which components are used so that I…

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## [Registering several non-orthogonal slices into volume](https://discourse.itk.org/t/registering-several-non-orthogonal-slices-into-volume/1976)

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**Author:** [@SMT](https://discourse.itk.org/u/SMT)\
**Replies:** 2\
**Last updated:** [June 18, 2019, 3:11pm UTC](https://discourse.itk.org/t/registering-several-non-orthogonal-slices-into-volume/1976 "2019-06-18T15:11:59Z")

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Hello, I am using ITK and SimpleITK in Python. I would like to register multiple slices with known relative orientation into a volume. I found this page with similar topic https://itk.org/pipermail/community/2014-Septem…

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## [Support for complex pixel type in SimpleITK is lacking](https://discourse.itk.org/t/support-for-complex-pixel-type-in-simpleitk-is-lacking/1942)

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**Author:** [@Brynolf](https://discourse.itk.org/u/Brynolf)\
**Replies:** 7\
**Last updated:** [June 13, 2019, 4:08pm UTC](https://discourse.itk.org/t/support-for-complex-pixel-type-in-simpleitk-is-lacking/1942 "2019-06-13T16:08:35Z")

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Hello, I have been dabbling with SimpleITK in python for a while now, and just now I ran in to an issue I cannot find the answer to. From the documentation it is possible to create images with complex type (sitkComplexF…

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## [Why itk::BSpineTransform add two extra control points to the upper bound?](https://discourse.itk.org/t/why-itk-bspinetransform-add-two-extra-control-points-to-the-upper-bound/1915)

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**Author:** [@sedghi](https://discourse.itk.org/u/sedghi)\
**Replies:** 3\
**Last updated:** [June 11, 2019, 1:09pm UTC](https://discourse.itk.org/t/why-itk-bspinetransform-add-two-extra-control-points-to-the-upper-bound/1915 "2019-06-11T13:09:08Z")

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I have a question regarding the extra control points that gets added to the grid for the B-spline transformation. I fully understand the one control point that gets added to the lower bound, but I don’t get why two cont…

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## [Registration Using Elastix-- Mutual Information based for CT volume to CT volume](https://discourse.itk.org/t/registration-using-elastix-mutual-information-based-for-ct-volume-to-ct-volume/1944)

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**Author:** [@srbn.ghosh89](https://discourse.itk.org/u/srbn.ghosh89)\
**Replies:** 4\
**Last updated:** [June 6, 2019, 2:21pm UTC](https://discourse.itk.org/t/registration-using-elastix-mutual-information-based-for-ct-volume-to-ct-volume/1944 "2019-06-06T14:21:53Z")

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There are lots of modules under elastix. Which module should I use for CT volume to CT volume registration? And where to put the input file names and how to choose the method?

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## [dimension images](https://discourse.itk.org/t/dimension-images/1890)

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**Author:** [@safa](https://discourse.itk.org/u/safa)\
**Replies:** 2\
**Last updated:** [May 18, 2019, 3:52pm UTC](https://discourse.itk.org/t/dimension-images/1890 "2019-05-18T15:52:20Z")

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i can’t upload the segmentation image with the main image any solution please to match the segmentation image with the main image !!!

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## [GPU Registration - Mutual Information](https://discourse.itk.org/t/gpu-registration-mutual-information/1779)

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**Author:** [@Knut](https://discourse.itk.org/u/Knut)\
**Replies:** 1\
**Last updated:** [May 1, 2019, 4:35pm UTC](https://discourse.itk.org/t/gpu-registration-mutual-information/1779 "2019-05-01T16:35:08Z")

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Hello, by GPUDemonsRegistrationFilter (itk 4.9.1) I was able to set up image registration.Registration results are really nice after fine tuning of parameters: SetMaximumError(0.08), SetMaximumKernelWidth(10) and SetInt…

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## [ITK5 - Bug in itkPolygonSpatialObject (SpatialObjectToImage3.cxx)](https://discourse.itk.org/t/itk5-bug-in-itkpolygonspatialobject-spatialobjecttoimage3-cxx/1774)

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**Author:** [@johnaddams](https://discourse.itk.org/u/johnaddams)\
**Replies:** 9\
**Last updated:** [April 25, 2019, 12:45am UTC](https://discourse.itk.org/t/itk5-bug-in-itkpolygonspatialobject-spatialobjecttoimage3-cxx/1774 "2019-04-25T00:45:19Z")

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The example SpatialObjectToImage3.cxx does not create a binary image from a polygon using the new ITKv5, it only generates black images. The problem is probably in itkPolygonSpatialObject. Other spatial objects (i.e. itk…

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## [How to convert image to png series?](https://discourse.itk.org/t/how-to-convert-image-to-png-series/1799)

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**Author:** [@srbn.ghosh89](https://discourse.itk.org/u/srbn.ghosh89)\
**Replies:** 1\
**Last updated:** [April 18, 2019, 12:37pm UTC](https://discourse.itk.org/t/how-to-convert-image-to-png-series/1799 "2019-04-18T12:37:28Z")

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Hi, In patient skull dicom data, there are 3 types of information, axial, coronal, saggital. I want to split these 3 types of image separately. How to do that using ITK?

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## [How to upload itk image to server?](https://discourse.itk.org/t/how-to-upload-itk-image-to-server/1766)

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**Author:** [@Andrzej\_Marciniak](https://discourse.itk.org/u/Andrzej_Marciniak)\
**Replies:** 2\
**Last updated:** [April 9, 2019, 10:05pm UTC](https://discourse.itk.org/t/how-to-upload-itk-image-to-server/1766 "2019-04-09T22:05:08Z")

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Hello, I am writing VTK/ITK MRI browser/editor and I would like to save edited image on a server. I found out how to convert vtk to itk (https://github.com/Kitware/paraview-glance/issues/180#issuecomment-408659132) , an…

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## [Memory problem loading vtk and itk](https://discourse.itk.org/t/memory-problem-loading-vtk-and-itk/1722)

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**Author:** [@zandarina](https://discourse.itk.org/u/zandarina)\
**Replies:** 11\
**Last updated:** [April 3, 2019, 9:18pm UTC](https://discourse.itk.org/t/memory-problem-loading-vtk-and-itk/1722 "2019-04-03T21:18:53Z")

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Dear all, I have a volume 549x549x700. I loaded in vtk and when i want to perform a segmentation, i export the vtk volume into a itk image but i get a memry problem. Is there any ay to share the object and not to cerat…

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## [ImageAlgorithm backward incompatible change](https://discourse.itk.org/t/imagealgorithm-backward-incompatible-change/1725)

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**Author:** [@simon.rit](https://discourse.itk.org/u/simon.rit)\
**Replies:** 1\
**Last updated:** [April 2, 2019, 3:15am UTC](https://discourse.itk.org/t/imagealgorithm-backward-incompatible-change/1725 "2019-04-02T03:15:16Z")

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The following commit has introduced a backward incompatible change (see for example RTK’s issues). Is this intentional? I have the feeling that defining a default template would have avoided this… but I’m guessing I’…

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## [Unknown tags reading tiff](https://discourse.itk.org/t/unknown-tags-reading-tiff/1719)

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**Author:** [@Gib](https://discourse.itk.org/u/Gib)\
**Replies:** 7\
**Last updated:** [April 1, 2019, 3:08am UTC](https://discourse.itk.org/t/unknown-tags-reading-tiff/1719 "2019-04-01T03:08:04Z")

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I have received a 3D tiff file that gives me warnings about unknown tags when I try to read it with ImageFileReader in ITK 4.12.2. The unknown tags are: 50838, 50839. The execution is stopped with no other information …

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## [skeletonize 3D liver vessels](https://discourse.itk.org/t/skeletonize-3d-liver-vessels/1711)

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**Author:** [@Marco\_Festugato](https://discourse.itk.org/u/Marco_Festugato)\
**Replies:** 1\
**Last updated:** [March 26, 2019, 5:38pm UTC](https://discourse.itk.org/t/skeletonize-3d-liver-vessels/1711 "2019-03-26T17:38:53Z")

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I guys, I have to skeletonize a 3D vascular net of the liver vessels. Any ideas/code/examples that could help me? I know that it exists the class itkBinaryThinningImageFilter but it works only for 2D images… Thanks in a…

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