# Latest

**URL:** https://discourse.itk.org/latest.md?page=64

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

**Page:** 65

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## [question about metric setter](https://discourse.itk.org/t/question-about-metric-setter/3251)

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**Author:** [@pierrectl](https://discourse.itk.org/u/pierrectl)\
**Replies:** 5\
**Last updated:** [July 3, 2020, 6:42am UTC](https://discourse.itk.org/t/question-about-metric-setter/3251 "2020-07-03T06:42:49Z")

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Hi everyone, I went through itkMeanSquaresImageToImageMetric.hxx file, and I was wondering what is the effect of changing this-\>SetUseAllPixels(true) to this-\>SetUseAllPixels(false)? Thank you in advance for your r…

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## [How can I use ITK quickly reads DICOM file sequence and reconstructs it?](https://discourse.itk.org/t/how-can-i-use-itk-quickly-reads-dicom-file-sequence-and-reconstructs-it/3250)

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**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 4\
**Last updated:** [July 3, 2020, 3:07am UTC](https://discourse.itk.org/t/how-can-i-use-itk-quickly-reads-dicom-file-sequence-and-reconstructs-it/3250 "2020-07-03T03:07:11Z")

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How can I use ITK quickly reads DICOM file sequence and reconstructs it? Can I use multi thread or Segmented reading? And now I just read dicom file sequence by ITK::ImageReader::SetDirectoryName and update()

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## [SimpleITK 2.0 Release Candidate 2](https://discourse.itk.org/t/simpleitk-2-0-release-candidate-2/3257)

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**Author:** [@blowekamp](https://discourse.itk.org/u/blowekamp)\
**Replies:** 0\
**Last updated:** [July 2, 2020, 8:02pm UTC](https://discourse.itk.org/t/simpleitk-2-0-release-candidate-2/3257 "2020-07-02T20:02:31Z")

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Announcement Announcing the SimpleITK 2.0 Release Candidate 2! This RC contains backwards incompatible changes. Users are encouraged to test the RC with their code and report back bugs and issues. This update contains …

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## [Edit mask shape (add/remove pixels) using sitk](https://discourse.itk.org/t/edit-mask-shape-add-remove-pixels-using-sitk/3245)

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**Author:** [@3omarkamal](https://discourse.itk.org/u/3omarkamal)\
**Replies:** 2\
**Last updated:** [July 2, 2020, 11:24am UTC](https://discourse.itk.org/t/edit-mask-shape-add-remove-pixels-using-sitk/3245 "2020-07-02T11:24:08Z")

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I have multiple image sets with manually drawn masks (using ITK snap) and I want to edit the shape of the masks using simpleITK. For example, I tried sitk.BinaryDilate(label,1) to grow the regions by one pixel at the bou…

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## [How to determine if the curve is closed?](https://discourse.itk.org/t/how-to-determine-if-the-curve-is-closed/3237)

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**Author:** [@guo7212](https://discourse.itk.org/u/guo7212)\
**Replies:** 3\
**Last updated:** [July 2, 2020, 11:06am UTC](https://discourse.itk.org/t/how-to-determine-if-the-curve-is-closed/3237 "2020-07-02T11:06:15Z")

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Hi all, I want to find the markers in CT scout. Is it possible to determine if the curve is closed?

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## [How is computed the Geometric Center of an Image](https://discourse.itk.org/t/how-is-computed-the-geometric-center-of-an-image/3247)

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**Author:** [@Luis\_Carlos\_Carneiro](https://discourse.itk.org/u/Luis_Carlos_Carneiro)\
**Replies:** 1\
**Last updated:** [July 1, 2020, 8:09pm UTC](https://discourse.itk.org/t/how-is-computed-the-geometric-center-of-an-image/3247 "2020-07-01T20:09:14Z")

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Dear All, Just for tuning. How is computed the geometric center of an image? For example, for one of the dimensions: DimX \>\> 1 (integer) float(DIMX -1)/2.0 (float or double) Thanks, Luis Gonçalves

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## [Registration of two space closed Images](https://discourse.itk.org/t/registration-of-two-space-closed-images/3228)

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**Author:** [@Luis\_Carlos\_Carneiro](https://discourse.itk.org/u/Luis_Carlos_Carneiro)\
**Replies:** 8\
**Last updated:** [June 30, 2020, 10:11pm UTC](https://discourse.itk.org/t/registration-of-two-space-closed-images/3228 "2020-06-30T22:11:17Z")

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Dear All, Happens that I take the Region of Interest of two images. Those images are space closed. I apply a Registration in Rotation and Translation (Mutual Information) and with the registration the result is worst t…

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## [Better positions of the subjects of registration](https://discourse.itk.org/t/better-positions-of-the-subjects-of-registration/3240)

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**Author:** [@Luis\_Carlos\_Carneiro](https://discourse.itk.org/u/Luis_Carlos_Carneiro)\
**Replies:** 3\
**Last updated:** [June 30, 2020, 6:17pm UTC](https://discourse.itk.org/t/better-positions-of-the-subjects-of-registration/3240 "2020-06-30T18:17:19Z")

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Dear All, I am using the following example. http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/Python\_html/60\_Registration\_Introduction.html I have the following doubt. If I want to do the registration of …

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## [InPlace and Order of the Operations in Transform](https://discourse.itk.org/t/inplace-and-order-of-the-operations-in-transform/3232)

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**Author:** [@Luis\_Carlos\_Carneiro](https://discourse.itk.org/u/Luis_Carlos_Carneiro)\
**Replies:** 8\
**Last updated:** [June 29, 2020, 10:25pm UTC](https://discourse.itk.org/t/inplace-and-order-of-the-operations-in-transform/3232 "2020-06-29T22:25:43Z")

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Dear All, By the manual I do not understand the difference between InPlace True and False. Could you please explain? What it is adequate. ##Don’t optimize in-place, we would possibly like to run this cell multiple tim…

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## [How to handle duplicte DICOM slices using SimpleITK?](https://discourse.itk.org/t/how-to-handle-duplicte-dicom-slices-using-simpleitk/3224)

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**Author:** [@mattwarkentin](https://discourse.itk.org/u/mattwarkentin)\
**Replies:** 12\
**Last updated:** [June 29, 2020, 4:10pm UTC](https://discourse.itk.org/t/how-to-handle-duplicte-dicom-slices-using-simpleitk/3224 "2020-06-29T16:10:46Z")

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Hi, This isn’t strictly a SimpleITK issue, but I am wondering how to handle such an issue using SimpleITK. I have been given axial CT from a colleague (stored in DICOM format), and it contains 146 slices of dimension 51…

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## [Registration in one Rotation parameters of the transform not doing well](https://discourse.itk.org/t/registration-in-one-rotation-parameters-of-the-transform-not-doing-well/3215)

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**Author:** [@Luis\_Carlos\_Carneiro](https://discourse.itk.org/u/Luis_Carlos_Carneiro)\
**Replies:** 9\
**Last updated:** [June 29, 2020, 2:33pm UTC](https://discourse.itk.org/t/registration-in-one-rotation-parameters-of-the-transform-not-doing-well/3215 "2020-06-29T14:33:58Z")

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Dear All, I am using the following example for my own purposes (but with Similarity3DTransform) : http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/Python\_html/60\_Registration\_Introduction.html When I do …

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## [Creating a coefficient image from mask](https://discourse.itk.org/t/creating-a-coefficient-image-from-mask/3236)

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**Author:** [@Michael\_Ef](https://discourse.itk.org/u/Michael_Ef)\
**Replies:** 2\
**Last updated:** [June 29, 2020, 1:22pm UTC](https://discourse.itk.org/t/creating-a-coefficient-image-from-mask/3236 "2020-06-29T13:22:32Z")

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Hi all, what is the best way to create a coefficient image (in mhd format) with values between 0 and 1 from a segmented image (grayscale)? E.g. every pixel on the reference image with value 100 will hold the value 0.4 i…

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## [Unable to use Fiji/ImageJ](https://discourse.itk.org/t/unable-to-use-fiji-imagej/3231)

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**Author:** [@ChocoLite](https://discourse.itk.org/u/ChocoLite)\
**Replies:** 1\
**Last updated:** [June 26, 2020, 12:47pm UTC](https://discourse.itk.org/t/unable-to-use-fiji-imagej/3231 "2020-06-26T12:47:38Z")

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Hi, I am trying to run setup.ipynb from the ISBI '20 tutorial on my computer. But, I’m getting the following error. I have installed Fiji Viewer on Ubuntu. The Fiji.app folder in my home directory (~/Fiji.app). I’m ve…

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## [Read ROIs from Dicom file and convert to pixel index](https://discourse.itk.org/t/read-rois-from-dicom-file-and-convert-to-pixel-index/3223)

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**Author:** [@malteekj](https://discourse.itk.org/u/malteekj)\
**Replies:** 4\
**Last updated:** [June 25, 2020, 1:20pm UTC](https://discourse.itk.org/t/read-rois-from-dicom-file-and-convert-to-pixel-index/3223 "2020-06-25T13:20:58Z")

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I’m trying to extract ROIs from Dicom files and convert the coordinates from mm in the patient coordinate system to a pixel indexes on the CT 3D array. The ROIs are saved in their own dicom files, and were drawn on the C…

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## [Struggling to do simple 3D rigid registration](https://discourse.itk.org/t/struggling-to-do-simple-3d-rigid-registration/3217)

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**Author:** [@msb](https://discourse.itk.org/u/msb)\
**Replies:** 4\
**Last updated:** [June 24, 2020, 11:54pm UTC](https://discourse.itk.org/t/struggling-to-do-simple-3d-rigid-registration/3217 "2020-06-24T23:54:14Z")

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Hello, I’m am struggling to perform a simple 3D rigid registration between 2 images. I have started with one of the tutorials, and tried to adapt it to my situation. Particularly I want to adjust it to do a rigid regist…

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## [How to create binary image from CT image.](https://discourse.itk.org/t/how-to-create-binary-image-from-ct-image/3222)

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**Author:** [@unicorn](https://discourse.itk.org/u/unicorn)\
**Replies:** 1\
**Last updated:** [June 24, 2020, 4:14pm UTC](https://discourse.itk.org/t/how-to-create-binary-image-from-ct-image/3222 "2020-06-24T16:14:05Z")

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I applied Sobel edge detector and wanted to apply threshold on it. How do I set these threshold? What are the values to be given here for CT?

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## [Cmake finding wrong compiler in my ITK project but finds correct compiler in ITK library?](https://discourse.itk.org/t/cmake-finding-wrong-compiler-in-my-itk-project-but-finds-correct-compiler-in-itk-library/3220)

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**Author:** [@rcatwood](https://discourse.itk.org/u/rcatwood)\
**Replies:** 10\
**Last updated:** [June 24, 2020, 3:06pm UTC](https://discourse.itk.org/t/cmake-finding-wrong-compiler-in-my-itk-project-but-finds-correct-compiler-in-itk-library/3220 "2020-06-24T15:06:04Z")

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Hi, This problem did not happen several weeks ago but it happens now. I am at a large installation with lots of linux workstations administered centrally. The choice of the administratiors is that all workstations hav…

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## [Express AffineTransform as single 4x4 matrix](https://discourse.itk.org/t/express-affinetransform-as-single-4x4-matrix/3193)

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**Author:** [@T\_Kirk](https://discourse.itk.org/u/T_Kirk)\
**Replies:** 16\
**Last updated:** [June 23, 2020, 11:36am UTC](https://discourse.itk.org/t/express-affinetransform-as-single-4x4-matrix/3193 "2020-06-23T11:36:19Z")

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I have an AffineTransform ITK object that I would like to use with other registration tools. To do so, I need to express the transform as a single 4x4 matrix in world-world terms - that is, incorporating all the Paramete…

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## [GPU memory leakage for GPUDemonsRegistrationFilter](https://discourse.itk.org/t/gpu-memory-leakage-for-gpudemonsregistrationfilter/3129)

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**Author:** [@qiang-zhang-neu](https://discourse.itk.org/u/qiang-zhang-neu)\
**Replies:** 9\
**Last updated:** [June 22, 2020, 5:34am UTC](https://discourse.itk.org/t/gpu-memory-leakage-for-gpudemonsregistrationfilter/3129 "2020-06-22T05:34:44Z")

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I need to use GPUDemonsRegistrationFilter in my project. However, I find it would cause gpu memory leakage. This problem can be repeated by the following code: #include "itkGPUDemonsRegistrationFilter.h" #include "itkHi…

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## [ITK 5.1.0 has been released!](https://discourse.itk.org/t/itk-5-1-0-has-been-released/3164)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 3\
**Last updated:** [June 22, 2020, 4:21am UTC](https://discourse.itk.org/t/itk-5-1-0-has-been-released/3164 "2020-06-22T04:21:07Z")

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We are happy to announce the Insight Toolkit (ITK) 5.1.0 release! :tada: ITK is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and registration. ITK 5.1.0 is a featur…

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## [Are the shift parameters affected by the scale parameter in the Similarity3DTransform](https://discourse.itk.org/t/are-the-shift-parameters-affected-by-the-scale-parameter-in-the-similarity3dtransform/3213)

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**Author:** [@Luis\_Carlos\_Carneiro](https://discourse.itk.org/u/Luis_Carlos_Carneiro)\
**Replies:** 3\
**Last updated:** [June 21, 2020, 2:13pm UTC](https://discourse.itk.org/t/are-the-shift-parameters-affected-by-the-scale-parameter-in-the-similarity3dtransform/3213 "2020-06-21T14:13:13Z")

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Dear All, I am using the Similarity3DTransform in SimpleITK. I have a doubt. After I get the transform, the parameters concerning the shift are with the dimensions of the .mhd file or the new ones affected by the scalin…

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## [Difference between ShrinkFactorPerLevel and Shrink](https://discourse.itk.org/t/difference-between-shrinkfactorperlevel-and-shrink/3189)

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**Author:** [@reox](https://discourse.itk.org/u/reox)\
**Replies:** 3\
**Last updated:** [June 19, 2020, 1:09pm UTC](https://discourse.itk.org/t/difference-between-shrinkfactorperlevel-and-shrink/3189 "2020-06-19T13:09:06Z")

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I want to register some images, however the image size is too fine for my purposes and lower resolutions do need less memory and registration time. Resizing them to a 10th of the size should also work. I tried now two d…

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## [Update image with itkwidget view 3D data](https://discourse.itk.org/t/update-image-with-itkwidget-view-3d-data/3202)

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**Author:** [@emilljungberg](https://discourse.itk.org/u/emilljungberg)\
**Replies:** 3\
**Last updated:** [June 19, 2020, 12:44am UTC](https://discourse.itk.org/t/update-image-with-itkwidget-view-3d-data/3202 "2020-06-19T00:44:47Z")

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Hi! I’ve recently started using the Python bindings for the latest version of ITK and it is working really great so far! I’m currently building an interactive application for testing effects of different filters with m…

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## [Call for Papers - MICCAI’20 Workshop on Shape Analysis in Medical Imaging (SHAPEMI)](https://discourse.itk.org/t/call-for-papers-miccai-20-workshop-on-shape-analysis-in-medical-imaging-shapemi/3203)

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**Author:** [@bpaniagua](https://discourse.itk.org/u/bpaniagua)\
**Replies:** 0\
**Last updated:** [June 18, 2020, 2:32pm UTC](https://discourse.itk.org/t/call-for-papers-miccai-20-workshop-on-shape-analysis-in-medical-imaging-shapemi/3203 "2020-06-18T14:32:01Z")

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MICCAI’20 SHAPEMI Workshop on Shape Analysis in Medical Imaging https://shapemi.github.io/ (\*) Description We gladly announce the second workshop for Shape Analysis in Medical Imaging (SHAPEMI, https://shapemi.gith…

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## [How to get Statistics data in a region with non zero values](https://discourse.itk.org/t/how-to-get-statistics-data-in-a-region-with-non-zero-values/3200)

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**Author:** [@Hasna\_R](https://discourse.itk.org/u/Hasna_R)\
**Replies:** 5\
**Last updated:** [June 18, 2020, 12:30pm UTC](https://discourse.itk.org/t/how-to-get-statistics-data-in-a-region-with-non-zero-values/3200 "2020-06-18T12:30:15Z")

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I have a 3D label object collection.From that I need to find min max and mean value in another volume of same dimension. For that i took bounding box from label object and extracted the region from volume and used itk …

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## [vcpkg Problems](https://discourse.itk.org/t/vcpkg-problems/3151)

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**Author:** [@spinicist](https://discourse.itk.org/u/spinicist)\
**Replies:** 8\
**Last updated:** [June 18, 2020, 8:59am UTC](https://discourse.itk.org/t/vcpkg-problems/3151 "2020-06-18T08:59:44Z")

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Hello, I’ve just tried to move my main project over to vcpkg. I’ve had two problems. First is that the $ITK\_LIBRARIES variable appears to be set incorrectly. It ends up being: ITK\_LIBRARIES="ITKLabelMap;ITKCommon;ITKS…

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## [AttributeError: module 'SimpleITK' has no attribute 'CompositeTransform'](https://discourse.itk.org/t/attributeerror-module-simpleitk-has-no-attribute-compositetransform/3188)

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**Author:** [@prms](https://discourse.itk.org/u/prms)\
**Replies:** 2\
**Last updated:** [June 18, 2020, 5:53am UTC](https://discourse.itk.org/t/attributeerror-module-simpleitk-has-no-attribute-compositetransform/3188 "2020-06-18T05:53:32Z")

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I’ve been using SimpleITK 1.2.4 and trying out the notebooks. In the notebook, I am getting the error AttributeError: module 'SimpleITK' has no attribute 'CompositeTransform' Is this some version mismatch issue or am I …

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## [Good procedures to get a good registration](https://discourse.itk.org/t/good-procedures-to-get-a-good-registration/3199)

<div class="topic-metadata">

**Author:** [@Luis\_Carlos\_Carneiro](https://discourse.itk.org/u/Luis_Carlos_Carneiro)\
**Replies:** 1\
**Last updated:** [June 17, 2020, 7:23pm UTC](https://discourse.itk.org/t/good-procedures-to-get-a-good-registration/3199 "2020-06-17T19:23:17Z")

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Dear All, I found out that there are some variance in the resulting parameters of the transforms of multiple registrations. How I can procedure to obtain always about the same results? Thanks, Luis Gonçalves

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## [BUG: module 'TubeTK' has no attribute 'swig'](https://discourse.itk.org/t/bug-module-tubetk-has-no-attribute-swig/2947)

<div class="topic-metadata">

**Author:** [@TaoH](https://discourse.itk.org/u/TaoH)\
**Replies:** 11\
**Last updated:** [June 17, 2020, 6:24pm UTC](https://discourse.itk.org/t/bug-module-tubetk-has-no-attribute-swig/2947 "2020-06-17T18:24:33Z")

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Hello, Thanks for your effort for InsightToolkit-5.1rc3! And I have installed tubetk with pip install itk-tubetk. The bug was reported when I tested the example ConvertTubesToImage.ipynb How can I handle the problem…

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## [itk & using them in CLI/C++ wrapper projects](https://discourse.itk.org/t/itk-using-them-in-cli-c-wrapper-projects/3198)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 0\
**Last updated:** [June 17, 2020, 3:36pm UTC](https://discourse.itk.org/t/itk-using-them-in-cli-c-wrapper-projects/3198 "2020-06-17T15:36:09Z")

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Hi all, I am trying to use c++/cli wrapper application to wrap around the c++ classes of ITK in order to call them from c# applications. I see simpleitk wrappers for the c# missing different classes so I want to build …

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