# Latest

**URL:** https://discourse.itk.org/latest.md?page=60

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

**Page:** 61

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## [Comparing Vector Images?](https://discourse.itk.org/t/comparing-vector-images/3517)

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**Author:** [@crocodoyle](https://discourse.itk.org/u/crocodoyle)\
**Replies:** 2\
**Last updated:** [October 8, 2020, 9:48pm UTC](https://discourse.itk.org/t/comparing-vector-images/3517 "2020-10-08T21:48:37Z")

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Hello, I have two vector images of type itk::Image\<itk::Vector\<double, 3\>\> that I am trying to compare for similarity. My first two approaches failed and I’m not sure why… First, I found the itk::Testing::ComparisonImag…

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## [Struggling to identify a coordinate from the original volume to the new resampled euler transform volume (with offset)](https://discourse.itk.org/t/struggling-to-identify-a-coordinate-from-the-original-volume-to-the-new-resampled-euler-transform-volume-with-offset/3515)

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**Author:** [@Helena](https://discourse.itk.org/u/Helena)\
**Replies:** 4\
**Last updated:** [October 7, 2020, 6:35pm UTC](https://discourse.itk.org/t/struggling-to-identify-a-coordinate-from-the-original-volume-to-the-new-resampled-euler-transform-volume-with-offset/3515 "2020-10-07T18:35:29Z")

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I have a volume that I resample using img\_center , and a transform matrix = \[0.814277854168591, 0.58047530198157, 0, -0.58047530198157, 0.814277854168591, 0, 0, 0, 1\] via euler 3d transformation. I would like to extract…

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## [stream writing in coronal orientation](https://discourse.itk.org/t/stream-writing-in-coronal-orientation/3514)

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**Author:** [@nikolay929](https://discourse.itk.org/u/nikolay929)\
**Replies:** 2\
**Last updated:** [October 7, 2020, 9:33am UTC](https://discourse.itk.org/t/stream-writing-in-coronal-orientation/3514 "2020-10-07T09:33:58Z")

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Hi. I’ve got several mha files, each is the subvolume of the big 3d volume. These subvolumes go in coronal direction. So, I need to combine them into one big file, but I don’t have enough memory to create whole image to…

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## [Bi variate polynomial warping filter?](https://discourse.itk.org/t/bi-variate-polynomial-warping-filter/3512)

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**Author:** [@rfrank](https://discourse.itk.org/u/rfrank)\
**Replies:** 2\
**Last updated:** [October 5, 2020, 4:05pm UTC](https://discourse.itk.org/t/bi-variate-polynomial-warping-filter/3512 "2020-10-05T16:05:51Z")

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I have coefficients a b for a polynomial X = a0 + a1x + a2y +a3xy + a4x^2 + a5y^2 Y = b0 +b1x + b2y + b3xy + b4x^2 + b5y^2 I would imagine there is an ITK filter for this type of transformation but I don’t seem to f…

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## [how to use itk c++ in jupiter notebooks?](https://discourse.itk.org/t/how-to-use-itk-c-in-jupiter-notebooks/3511)

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**Author:** [@unicorn](https://discourse.itk.org/u/unicorn)\
**Replies:** 1\
**Last updated:** [October 5, 2020, 9:15am UTC](https://discourse.itk.org/t/how-to-use-itk-c-in-jupiter-notebooks/3511 "2020-10-05T09:15:57Z")

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I have recently got to know that, we can use jupyter notebooks for running c++ codes also. How can we import ITK into it?

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## [How to use itk::AffineTransform::Rotate3D in python?](https://discourse.itk.org/t/how-to-use-itk-rotate3d-in-python/3503)

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**Author:** [@ghf](https://discourse.itk.org/u/ghf)\
**Replies:** 1\
**Last updated:** [October 2, 2020, 2:37pm UTC](https://discourse.itk.org/t/how-to-use-itk-rotate3d-in-python/3503 "2020-10-02T14:37:17Z")

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How to use itk::AffineTransform::Rotate3D in python?

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## [Datatype error](https://discourse.itk.org/t/datatype-error/3499)

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**Author:** [@Romy\_Meester](https://discourse.itk.org/u/Romy_Meester)\
**Replies:** 2\
**Last updated:** [October 1, 2020, 3:03pm UTC](https://discourse.itk.org/t/datatype-error/3499 "2020-10-01T15:03:38Z")

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Hello, I try to implement several filters in SITK for 3D images, but I do get an error with the Anisotropic diffusion image filter. (The Gaussian, median and curvature flow are working :slight\_smile: ) def calc\_anisot…

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## [Wiener deconvolution image filter](https://discourse.itk.org/t/wiener-deconvolution-image-filter/3498)

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**Author:** [@Romy\_Meester](https://discourse.itk.org/u/Romy_Meester)\
**Replies:** 1\
**Last updated:** [October 1, 2020, 1:34pm UTC](https://discourse.itk.org/t/wiener-deconvolution-image-filter/3498 "2020-10-01T13:34:41Z")

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Hello, I try to implement several filters in SITK for 3D images, but I do get an error with the Wiener deconvolution image filter. (The Gaussian, median and curvature flow are working :slight\_smile: ) This is my functi…

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## [adjusting two different CT images in the same position](https://discourse.itk.org/t/adjusting-two-different-ct-images-in-the-same-position/3492)

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**Author:** [@Gokce\_Guven](https://discourse.itk.org/u/Gokce_Guven)\
**Replies:** 3\
**Last updated:** [September 30, 2020, 6:45pm UTC](https://discourse.itk.org/t/adjusting-two-different-ct-images-in-the-same-position/3492 "2020-09-30T18:45:55Z")

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Hi, I have approximately hundreds of extremity CT (.mhd files) which I want to orient in 3D space such that the images would be located in the middle of the volume and palms are looking to the same direction and save th…

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## [How can i reconstruct series or sequence of 2D DICOM images into 3D reconstruction?](https://discourse.itk.org/t/how-can-i-reconstruct-series-or-sequence-of-2d-dicom-images-into-3d-reconstruction/3495)

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**Author:** [@Yuvi-416](https://discourse.itk.org/u/Yuvi-416)\
**Replies:** 3\
**Last updated:** [September 30, 2020, 4:51pm UTC](https://discourse.itk.org/t/how-can-i-reconstruct-series-or-sequence-of-2d-dicom-images-into-3d-reconstruction/3495 "2020-09-30T16:51:18Z")

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Hello there, I had a bunch of microscopy image in a .tif or a .czi extension but I manage to convert it into Dicom standard format using pydicom. Moreover, after conversion now I have a sequence of Dicom image like from…

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## [SimpleITK - connecting to other image processing libraries](https://discourse.itk.org/t/simpleitk-connecting-to-other-image-processing-libraries/3491)

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**Author:** [@haesleinhuepf](https://discourse.itk.org/u/haesleinhuepf)\
**Replies:** 5\
**Last updated:** [September 29, 2020, 6:22pm UTC](https://discourse.itk.org/t/simpleitk-connecting-to-other-image-processing-libraries/3491 "2020-09-29T18:22:14Z")

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Hey all, @blowekamp @matt.mccormick first of all congrats to the developers for the SimpleITK 2.0 release! :partying\_face: I was just exploring it from Java and I’m wondering how to pipe pixels from another source int…

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## [How to print and stretch CT data value(the gray value)?](https://discourse.itk.org/t/how-to-print-and-stretch-ct-data-value-the-gray-value/3488)

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**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 2\
**Last updated:** [September 28, 2020, 8:29pm UTC](https://discourse.itk.org/t/how-to-print-and-stretch-ct-data-value-the-gray-value/3488 "2020-09-28T20:29:36Z")

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How to print and stretch CT data value(the gray value)?

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## [Adaptive denoising filter in ITK?](https://discourse.itk.org/t/adaptive-denoising-filter-in-itk/3480)

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**Author:** [@ntustison](https://discourse.itk.org/u/ntustison)\
**Replies:** 8\
**Last updated:** [September 28, 2020, 6:19pm UTC](https://discourse.itk.org/t/adaptive-denoising-filter-in-itk/3480 "2020-09-28T18:19:05Z")

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I’m guessing this is a question for @matt.mccormick and potentially others (e.g., @blowekamp @hjmjohnson). With the most recent FreeSurfer release, the developers added some ITK-based functionality originally developed…

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## [Filter a 3D image slice by slice and store results](https://discourse.itk.org/t/filter-a-3d-image-slice-by-slice-and-store-results/3484)

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**Author:** [@Elli](https://discourse.itk.org/u/Elli)\
**Replies:** 4\
**Last updated:** [September 25, 2020, 6:49pm UTC](https://discourse.itk.org/t/filter-a-3d-image-slice-by-slice-and-store-results/3484 "2020-09-25T18:49:11Z")

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Dear all, I have a 3D volume, I want to iterate over all 2D slices, apply a convolutional filter on each slice and then put them again together as a 3D volume and store this 3D volume. Somehow, I am failing to do so an…

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## [How to calculate Jacobian matrix of a transformation with simpleITK?](https://discourse.itk.org/t/how-to-calculate-jacobian-matrix-of-a-transformation-with-simpleitk/3486)

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**Author:** [@dada](https://discourse.itk.org/u/dada)\
**Replies:** 1\
**Last updated:** [September 25, 2020, 6:00pm UTC](https://discourse.itk.org/t/how-to-calculate-jacobian-matrix-of-a-transformation-with-simpleitk/3486 "2020-09-25T18:00:10Z")

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Hello, How to calculate Jacobian matrix at each pixel with simpleITK after I have estimated a B-spline transformation between fixed\_image and moving\_image? Do I need to convert the transformation into displacement fiel…

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## [Does SimpleITK return final transformation corresponding to the best similarity metric value or it return the final transformation obtained the last iteration?](https://discourse.itk.org/t/does-simpleitk-return-final-transformation-corresponding-to-the-best-similarity-metric-value-or-it-return-the-final-transformation-obtained-the-last-iteration/3428)

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**Author:** [@dada](https://discourse.itk.org/u/dada)\
**Replies:** 10\
**Last updated:** [September 25, 2020, 5:12pm UTC](https://discourse.itk.org/t/does-simpleitk-return-final-transformation-corresponding-to-the-best-similarity-metric-value-or-it-return-the-final-transformation-obtained-the-last-iteration/3428 "2020-09-25T17:12:25Z")

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Hello, I am doing B-spline registration with SimpleITK, and I set MeanSquares as similarity metric. Can I ask: does SimpleITK return final transformation corresponding to the best similarity metric value or it return t…

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## [Accelerators via executors in ITK](https://discourse.itk.org/t/accelerators-via-executors-in-itk/3456)

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**Author:** [@phcerdan](https://discourse.itk.org/u/phcerdan)\
**Replies:** 1\
**Last updated:** [September 25, 2020, 3:34pm UTC](https://discourse.itk.org/t/accelerators-via-executors-in-itk/3456 "2020-09-25T15:34:48Z")

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I have seen that Facebook (Niebler et al.) published an implementation about executors recently: libunifex. I heard about executors from @matt.mccormick, I was thinking about the steps that ITK would need to implement t…

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## [Invert a ScaleVersor3DTransform](https://discourse.itk.org/t/invert-a-scaleversor3dtransform/3483)

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**Author:** [@reox](https://discourse.itk.org/u/reox)\
**Replies:** 6\
**Last updated:** [September 25, 2020, 5:07am UTC](https://discourse.itk.org/t/invert-a-scaleversor3dtransform/3483 "2020-09-25T05:07:20Z")

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I tried to invert a ScaleVersor3DTransform, but I get this error message: \>\>\> import SimpleITK as sitk \>\>\> tx = sitk.ScaleVersor3DTransform() \>\>\> tx.SetTranslation(\[1,2,3\]) \>\>\> tx.SetScale(\[0.9, 1.1, 1.2\]) \>\>\> tx.GetInv…

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## [itk.js: readImageDICOMFile(Series): wrong componentType with itk.js 13.1.3](https://discourse.itk.org/t/itk-js-readimagedicomfile-series-wrong-componenttype-with-itk-js-13-1-3/3477)

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**Author:** [@Athius](https://discourse.itk.org/u/Athius)\
**Replies:** 2\
**Last updated:** [September 24, 2020, 2:13pm UTC](https://discourse.itk.org/t/itk-js-readimagedicomfile-series-wrong-componenttype-with-itk-js-13-1-3/3477 "2020-09-24T14:13:49Z")

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Hi, I tried to load a MRI DICOM series using readImageDICOMFileSeries in javascript. For this, I start from the itk-read-dicom example and update the itk package to the last version (13.1.3) and modify the line: return…

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## [GetDirection and GetOrigin for SimpleITK C# implementation](https://discourse.itk.org/t/getdirection-and-getorigin-for-simpleitk-c-implementation/3472)

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**Author:** [@Guilmer](https://discourse.itk.org/u/Guilmer)\
**Replies:** 8\
**Last updated:** [September 23, 2020, 7:54pm UTC](https://discourse.itk.org/t/getdirection-and-getorigin-for-simpleitk-c-implementation/3472 "2020-09-23T19:54:16Z")

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Hi, I am using the C# implementation for SimpleITK to display MRI data in the Unity game engine and I am running into issues with orientations and IJK to world transform matrices. My data is a nifti file in RAS coordin…

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## [SimpleITK 2.0 Release](https://discourse.itk.org/t/simpleitk-2-0-release/3482)

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**Author:** [@blowekamp](https://discourse.itk.org/u/blowekamp)\
**Replies:** 0\
**Last updated:** [September 23, 2020, 5:06pm UTC](https://discourse.itk.org/t/simpleitk-2-0-release/3482 "2020-09-23T17:06:29Z")

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Announcement SimpleITK 2.0 has been released! This major version update to SimpleITK includes updating to ITK version 5, significant code improvements, performance enhancements, and API changes. Installing SimpleITK Com…

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## ['itkMatrixD33' object does not support indexing](https://discourse.itk.org/t/itkmatrixd33-object-does-not-support-indexing/3479)

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**Author:** [@isuruwi](https://discourse.itk.org/u/isuruwi)\
**Replies:** 0\
**Last updated:** [September 22, 2020, 10:32am UTC](https://discourse.itk.org/t/itkmatrixd33-object-does-not-support-indexing/3479 "2020-09-22T10:32:36Z")

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I’m trying to implement the ComputeIndexToPhysicalPointMatrices functionality. I have initialized scale variable as below in python. (scale is a DirectionType variable in c++ code) scale = itk.Matrix.D33() And the tr…

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## [converting 3d .zraw image into 2d .png](https://discourse.itk.org/t/converting-3d-zraw-image-into-2d-png/3476)

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**Author:** [@abir](https://discourse.itk.org/u/abir)\
**Replies:** 2\
**Last updated:** [September 22, 2020, 5:30am UTC](https://discourse.itk.org/t/converting-3d-zraw-image-into-2d-png/3476 "2020-09-22T05:30:08Z")

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I used a python code to convert my 3d image into png images but an error occured. Someone suggested me to use Simple itk. for every 3d image I should get 3 2d images (axial,coronal and sagittal vue ) Can any one help m…

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## [Adding Patient position tag in each slice while writing a dicom series](https://discourse.itk.org/t/adding-patient-position-tag-in-each-slice-while-writing-a-dicom-series/3467)

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**Author:** [@Hasna](https://discourse.itk.org/u/Hasna)\
**Replies:** 6\
**Last updated:** [September 18, 2020, 3:21pm UTC](https://discourse.itk.org/t/adding-patient-position-tag-in-each-slice-while-writing-a-dicom-series/3467 "2020-09-18T15:21:14Z")

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Hi, I am trying generate a dicom series from volume data. How can should i give the patient position tag ,orientation tag and pixel spacing tag for each slice? Should I add them in a loop? I could not find any example…

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## [Change Pixel values of Images where expression](https://discourse.itk.org/t/change-pixel-values-of-images-where-expression/3465)

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**Author:** [@reox](https://discourse.itk.org/u/reox)\
**Replies:** 4\
**Last updated:** [September 17, 2020, 12:43pm UTC](https://discourse.itk.org/t/change-pixel-values-of-images-where-expression/3465 "2020-09-17T12:43:13Z")

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For example, I want to set all pixel values of an image to 1 where the current pixel value is \>1. In numpy, this could be done in the following way: x\[x \> 1\] = 1 However, for Images that does not work: # x -\> SimpleI…

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## [How to store certain indices in point set or a matrix?](https://discourse.itk.org/t/how-to-store-certain-indices-in-point-set-or-a-matrix/3459)

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**Author:** [@unicorn](https://discourse.itk.org/u/unicorn)\
**Replies:** 1\
**Last updated:** [September 14, 2020, 4:40pm UTC](https://discourse.itk.org/t/how-to-store-certain-indices-in-point-set-or-a-matrix/3459 "2020-09-14T16:40:05Z")

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I want to extract certain indices of segmentation from each slice of the image and store it in a point set or a matrix(I’m not sure which one to use). Upon that, I would like to perform singular value decomposition. How…

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## [link error. ld: library not found for -lITKVideoIO](https://discourse.itk.org/t/link-error-ld-library-not-found-for-litkvideoio/3461)

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**Author:** [@kaiyan\_liu](https://discourse.itk.org/u/kaiyan_liu)\
**Replies:** 1\
**Last updated:** [September 14, 2020, 4:37pm UTC](https://discourse.itk.org/t/link-error-ld-library-not-found-for-litkvideoio/3461 "2020-09-14T16:37:00Z")

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I’m new here for ITK. And I have tried to install ITK-5.2.0 My environment version is as follows : OS:macOS 10.15.6. CMake 3.17.3 Make 3.81 clang 6.0.0 I try to compile and install ITK as the guidebook (ItkSoftwareGuid…

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## [write euler2d transform to file](https://discourse.itk.org/t/write-euler2d-transform-to-file/3458)

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**Author:** [@Henco](https://discourse.itk.org/u/Henco)\
**Replies:** 1\
**Last updated:** [September 14, 2020, 4:31pm UTC](https://discourse.itk.org/t/write-euler2d-transform-to-file/3458 "2020-09-14T16:31:15Z")

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Hi all, I’m trying to use ImageRegistration5.cxx to register two 2d images. I’d like to have the program write the resultant transform to file so I can use it later in Slicer. I’m using the code below, and a file is bei…

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## [How to write a DicomVolume from a DicomSeries without losing Header Infos.](https://discourse.itk.org/t/how-to-write-a-dicomvolume-from-a-dicomseries-without-losing-header-infos/3443)

<div class="topic-metadata">

**Author:** [@Amnesie](https://discourse.itk.org/u/Amnesie)\
**Replies:** 16\
**Last updated:** [September 12, 2020, 6:14am UTC](https://discourse.itk.org/t/how-to-write-a-dicomvolume-from-a-dicomseries-without-losing-header-infos/3443 "2020-09-12T06:14:46Z")

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Hi everyone, I have read the DicomSeriesReadImageWrite2 example . It did work but i noticed the Dicom-header Infos are “losted”. All of slices have the same Dicom-header Infos and pixel spacing will be default 1. I ti…

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## [TransformPhysicalPointToIndex that remains inside the boundaries of the image](https://discourse.itk.org/t/transformphysicalpointtoindex-that-remains-inside-the-boundaries-of-the-image/3435)

<div class="topic-metadata">

**Author:** [@spyridon97](https://discourse.itk.org/u/spyridon97)\
**Replies:** 10\
**Last updated:** [September 10, 2020, 5:07pm UTC](https://discourse.itk.org/t/transformphysicalpointtoindex-that-remains-inside-the-boundaries-of-the-image/3435 "2020-09-10T17:07:53Z")

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Hello everyone, I am working with ITK images and I am using TransformPhysicalPointToIndex a lot!. My physical space bounds are quite strict, so I wanna be sure that this function computes accurately indices of points t…

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