# Latest

**URL:** https://discourse.itk.org/latest.md?page=51

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

**Page:** 52

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## [Save parameters for N4 bias field correction](https://discourse.itk.org/t/save-parameters-for-n4-bias-field-correction/3530)

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**Author:** [@federico\_nemmi](https://discourse.itk.org/u/federico_nemmi)\
**Replies:** 3\
**Last updated:** [October 23, 2020, 12:31pm UTC](https://discourse.itk.org/t/save-parameters-for-n4-bias-field-correction/3530 "2020-10-23T12:31:31Z")

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Hi, I have acquired a 6 points MRI Dixon sequence from which I have derived Water, Fat and Fat Fraction images. Since the derived images all come from the same original sequence, they all share the same field bias (at le…

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## [File format for general-purpose medical image computing](https://discourse.itk.org/t/file-format-for-general-purpose-medical-image-computing/4067)

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**Author:** [@lassoan](https://discourse.itk.org/u/lassoan)\
**Replies:** 17\
**Last updated:** [May 7, 2021, 11:21am UTC](https://discourse.itk.org/t/file-format-for-general-purpose-medical-image-computing/4067 "2021-05-07T11:21:20Z")

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We encounter so many issues due to redundancies and inconsistencies within the nifti file format. Am I alone with being frustrated by this? I try to educate users one by one to not use nifti except for brain imaging, but…

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## [Segmentation of aorta using itk](https://discourse.itk.org/t/segmentation-of-aorta-using-itk/4101)

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**Author:** [@priyanka](https://discourse.itk.org/u/priyanka)\
**Replies:** 3\
**Last updated:** [May 7, 2021, 6:26am UTC](https://discourse.itk.org/t/segmentation-of-aorta-using-itk/4101 "2021-05-07T06:26:18Z")

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I’m new to this topic. Suggest me best method for segmenting aorta from the series of dicoms using itk C++.

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## [ITK 5.2 Release Candidate 3 available for testing](https://discourse.itk.org/t/itk-5-2-release-candidate-3-available-for-testing/3947)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 3\
**Last updated:** [May 6, 2021, 6:56pm UTC](https://discourse.itk.org/t/itk-5-2-release-candidate-3-available-for-testing/3947 "2021-05-06T18:56:33Z")

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ITK 5.2 Release Candidate 3 Release Notes We are happy to announce the Insight Toolkit (ITK) 5.2 Release Candidate 3 is available for testing! :tada: ITK is an open-source, cross-platform toolkit for N-dimensional scient…

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## [itk-snap build from source needs older versions of ITK](https://discourse.itk.org/t/itk-snap-build-from-source-needs-older-versions-of-itk/4103)

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**Author:** [@colinbannister](https://discourse.itk.org/u/colinbannister)\
**Replies:** 2\
**Last updated:** [May 6, 2021, 2:24pm UTC](https://discourse.itk.org/t/itk-snap-build-from-source-needs-older-versions-of-itk/4103 "2021-05-06T14:24:12Z")

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Trying to build ITK-snap from source, as binaries do not run on our system. Looking at guide at BuildingITK-SNAP, it specifies versions of ITK that are needed. I have version 4.13.1 and 4.13.3, but not the actual versio…

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## [is gcc supported only](https://discourse.itk.org/t/is-gcc-supported-only/4098)

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**Author:** [@hfeng](https://discourse.itk.org/u/hfeng)\
**Replies:** 4\
**Last updated:** [May 5, 2021, 1:11pm UTC](https://discourse.itk.org/t/is-gcc-supported-only/4098 "2021-05-05T13:11:34Z")

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itk 5.1.2 is installed. In a generated file itk\_compiler\_detection.h, i saw a few lines: if ITK\_COMPILER\_IS\_GNU include “compilers/ITK\_COMPILER\_INFO\_GNU\_CXX.h” else error Unsupported compiler endif Does this mean only G…

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## [Add a rigid transform and a deformable transform together](https://discourse.itk.org/t/add-a-rigid-transform-and-a-deformable-transform-together/4083)

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**Author:** [@hfeng](https://discourse.itk.org/u/hfeng)\
**Replies:** 2\
**Last updated:** [May 4, 2021, 11:47pm UTC](https://discourse.itk.org/t/add-a-rigid-transform-and-a-deformable-transform-together/4083 "2021-05-04T23:47:31Z")

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I am trying to do a image registration that consists of two stages. The first stage is selected to be Versor3DRigid and the second stage is selected to be Demons. The first stage can give a transform, the second stage …

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## [BSpline registration for non-overlapping images](https://discourse.itk.org/t/bspline-registration-for-non-overlapping-images/4097)

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**Author:** [@ctorti](https://discourse.itk.org/u/ctorti)\
**Replies:** 0\
**Last updated:** [May 4, 2021, 9:02pm UTC](https://discourse.itk.org/t/bspline-registration-for-non-overlapping-images/4097 "2021-05-04T21:02:43Z")

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Having run into problems trying to use landmarks to initiate a bspline registration of 3D CT and MR images, I decided to try a workaround: I cropped the CT image such that the field of view (in all three directions) is …

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## [Apply Demons transformation onto an image.](https://discourse.itk.org/t/apply-demons-transformation-onto-an-image/4094)

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**Author:** [@eyalol](https://discourse.itk.org/u/eyalol)\
**Replies:** 3\
**Last updated:** [May 4, 2021, 12:58pm UTC](https://discourse.itk.org/t/apply-demons-transformation-onto-an-image/4094 "2021-05-04T12:58:35Z")

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Hello, This is my first time using SimpleITK, I’m interested in using the Demons registration algorithm, I’m using the python version of this: DemonsRegistration1 — SimpleITK 2.0rc2 documentation after applying the alg…

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## [How to get output of HoughTransform2DLinesImageFilter() ?](https://discourse.itk.org/t/how-to-get-output-of-houghtransform2dlinesimagefilter/4059)

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**Author:** [@YMarth](https://discourse.itk.org/u/YMarth)\
**Replies:** 7\
**Last updated:** [May 4, 2021, 3:00am UTC](https://discourse.itk.org/t/how-to-get-output-of-houghtransform2dlinesimagefilter/4059 "2021-05-04T03:00:51Z")

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I am trying to use Hough Lines transform on some iage with itk on python (spyder). I used the given example here: How to deal with HoughTransform2DLinesImageFilter GetLines() method in python - Beginner Questions - ITK …

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## [(coarse) point set registration in python](https://discourse.itk.org/t/coarse-point-set-registration-in-python/4044)

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**Author:** [@Johannes](https://discourse.itk.org/u/Johannes)\
**Replies:** 3\
**Last updated:** [May 3, 2021, 8:39pm UTC](https://discourse.itk.org/t/coarse-point-set-registration-in-python/4044 "2021-05-03T20:39:06Z")

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Hey there! I am a young researcher-to-be and I am currently working on my bachelor’s thesis. The problem, because of which I reach out to you, boils down to a point set registration of one xy and one xyz image with litt…

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## [Missing libITKIOGDCM-5.3.a file for GATE build](https://discourse.itk.org/t/missing-libitkiogdcm-5-3-a-file-for-gate-build/4090)

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**Author:** [@thestrangefruition](https://discourse.itk.org/u/thestrangefruition)\
**Replies:** 1\
**Last updated:** [May 3, 2021, 6:01pm UTC](https://discourse.itk.org/t/missing-libitkiogdcm-5-3-a-file-for-gate-build/4090 "2021-05-03T18:01:03Z")

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Hello all, I am attempting to install and compile GATE which used ITK alongside it. When running make to compile GATE, I get this error regarding a missing ITK file: strangefruition@WORK:~/Gate-9.1/gate\_v9.1-build$ mak…

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## [Using "short" data directly as input to the N4BiasFieldCorrectionImageFilter](https://discourse.itk.org/t/using-short-data-directly-as-input-to-the-n4biasfieldcorrectionimagefilter/4081)

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**Author:** [@Tamar](https://discourse.itk.org/u/Tamar)\
**Replies:** 2\
**Last updated:** [April 28, 2021, 3:16pm UTC](https://discourse.itk.org/t/using-short-data-directly-as-input-to-the-n4biasfieldcorrectionimagefilter/4081 "2021-04-28T15:16:13Z")

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I am incorporating the simpleITK N4BiasFieldCorrectionImageFilter into an existing c# application as part of the image processing chain. Is there is a way to read the input data directly from a “short” array that is sto…

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## [FastSymmetricForcesDemonsRegistrationFilter.SetUseImageSpacing() not working?](https://discourse.itk.org/t/fastsymmetricforcesdemonsregistrationfilter-setuseimagespacing-not-working/4080)

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**Author:** [@Arthur\_Masson](https://discourse.itk.org/u/Arthur_Masson)\
**Replies:** 3\
**Last updated:** [April 27, 2021, 5:16pm UTC](https://discourse.itk.org/t/fastsymmetricforcesdemonsregistrationfilter-setuseimagespacing-not-working/4080 "2021-04-27T17:16:26Z")

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It seems that FastSymmetricForcesDemonsRegistrationFilter.SetUseImageSpacing() does not work, I get the same result when setting it to True or False, and same thing with FastSymmetricForcesDemonsRegistrationFilter.UseIm…

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## [Display displacement field with SimpleITK](https://discourse.itk.org/t/display-displacement-field-with-simpleitk/4078)

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**Author:** [@Arthur\_Masson](https://discourse.itk.org/u/Arthur_Masson)\
**Replies:** 6\
**Last updated:** [April 27, 2021, 2:54pm UTC](https://discourse.itk.org/t/display-displacement-field-with-simpleitk/4078 "2021-04-27T14:54:02Z")

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How could I display a displacement field (in physical space) with arrows on an image slice with SimpleITK ? I tried using quiver in matplotlib, but I had troubles with the physical to voxel space conversions. Is there …

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## [inter-patient Registration](https://discourse.itk.org/t/inter-patient-registration/4063)

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**Author:** [@Michel\_Atieh](https://discourse.itk.org/u/Michel_Atieh)\
**Replies:** 5\
**Last updated:** [April 26, 2021, 6:04pm UTC](https://discourse.itk.org/t/inter-patient-registration/4063 "2021-04-26T18:04:09Z")

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Dear All, I have two CT scans, one is truncated it has only part of the abdomen and the thorax, the other one is of the whole body. Whenever I try to do the registration the resulting image is a truncated image whether…

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## [Could not run basic example code from ITK Resample Image filter](https://discourse.itk.org/t/could-not-run-basic-example-code-from-itk-resample-image-filter/4071)

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**Author:** [@fonis](https://discourse.itk.org/u/fonis)\
**Replies:** 1\
**Last updated:** [April 26, 2021, 8:57pm UTC](https://discourse.itk.org/t/could-not-run-basic-example-code-from-itk-resample-image-filter/4071 "2021-04-26T20:57:20Z")

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Using ITK v5.2. The basic resample filter example fails. Error: “Requested region is (at least partially) outside the largest possible region.” The code below is basically a cleaned up version of ResampleImageFilter.c…

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## [Trouble building Lesion Sizing Toolkit](https://discourse.itk.org/t/trouble-building-lesion-sizing-toolkit/4069)

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**Author:** [@clicq](https://discourse.itk.org/u/clicq)\
**Replies:** 1\
**Last updated:** [April 26, 2021, 8:59pm UTC](https://discourse.itk.org/t/trouble-building-lesion-sizing-toolkit/4069 "2021-04-26T20:59:34Z")

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I am having trouble trying to build the Lesion Sizing Toolkit module. I first tried the latest released version of ITK, 5.1.2, enabling the LesionSizingToolkit and ITKVTKglue modules. While the dependencies build correct…

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## [Jacobian determinant](https://discourse.itk.org/t/jacobian-determinant/4060)

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**Author:** [@Fleur](https://discourse.itk.org/u/Fleur)\
**Replies:** 4\
**Last updated:** [April 26, 2021, 7:59pm UTC](https://discourse.itk.org/t/jacobian-determinant/4060 "2021-04-26T19:59:56Z")

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Dear all, I’m trying to compute the Jacobian Determinant of a deformation field. The transformation and its deformation field were not computed with simple ITK. I simply applied sitk.DisplacementFieldJacobianDeterminan…

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## [Nifti: ImageFileReader + ImageFileWriter changes orientation matrix](https://discourse.itk.org/t/nifti-imagefilereader-imagefilewriter-changes-orientation-matrix/4064)

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**Author:** [@crossmanith](https://discourse.itk.org/u/crossmanith)\
**Replies:** 3\
**Last updated:** [April 26, 2021, 12:48pm UTC](https://discourse.itk.org/t/nifti-imagefilereader-imagefilewriter-changes-orientation-matrix/4064 "2021-04-26T12:48:22Z")

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Hi, I’m reading a Nifti File and writing it back without applying any other filter: using ReaderType = itk::ImageFileReader; ReaderType::Pointer in=ReaderType::New(); in-\>SetFileName( ifname ); in-\>Update(); using …

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## [Can LevenbergMarquardtOptimizer be constrained with bounds ?](https://discourse.itk.org/t/can-levenbergmarquardtoptimizer-be-constrained-with-bounds/4075)

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**Author:** [@agp](https://discourse.itk.org/u/agp)\
**Replies:** 0\
**Last updated:** [April 26, 2021, 9:32am UTC](https://discourse.itk.org/t/can-levenbergmarquardtoptimizer-be-constrained-with-bounds/4075 "2021-04-26T09:32:04Z")

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Hello everyone, I have been working on registering a statistical shape model to a 3D pointset, using ITK and statismo I have tested multiple optimizers available in ITK to optimize a composite transform of a itk::Stati…

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## [Get path of the mhd's data file](https://discourse.itk.org/t/get-path-of-the-mhds-data-file/4049)

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**Author:** [@reox](https://discourse.itk.org/u/reox)\
**Replies:** 6\
**Last updated:** [April 22, 2021, 1:32pm UTC](https://discourse.itk.org/t/get-path-of-the-mhds-data-file/4049 "2021-04-22T13:32:10Z")

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I use MetaImage files (mhd) a lot and sometimes need the path of the data file. Usually, I have the file loaded via SimpleITK already. Thus, is there a way to retrieve the name of the data file from the python interface …

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## [\[solved\] Disable python wrapping for a specific remote module](https://discourse.itk.org/t/solved-disable-python-wrapping-for-a-specific-remote-module/4055)

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**Author:** [@eric](https://discourse.itk.org/u/eric)\
**Replies:** 5\
**Last updated:** [April 20, 2021, 11:54pm UTC](https://discourse.itk.org/t/solved-disable-python-wrapping-for-a-specific-remote-module/4055 "2021-04-20T23:54:22Z")

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Hi, I’m trying to compile ITK with the remote module RTK and python wrapping. I’m having issues with building the RTK python wrapper with multiple symbol definition on Windows, I tried tackling it to no avail. In the m…

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## [How lightweight can this software be? (Plus few other questions...)](https://discourse.itk.org/t/how-lightweight-can-this-software-be-plus-few-other-questions/4051)

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**Author:** [@JamesBrown57](https://discourse.itk.org/u/JamesBrown57)\
**Replies:** 1\
**Last updated:** [April 20, 2021, 5:50pm UTC](https://discourse.itk.org/t/how-lightweight-can-this-software-be-plus-few-other-questions/4051 "2021-04-20T17:50:47Z")

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How lightweight can this software be until it loses all main functionality? For example, if I were to find an implementation of ITK (a library) within an application/software that processes pictures of tree roots to det…

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## [How to set the "Method" in ThresholdImageFilter in sitk](https://discourse.itk.org/t/how-to-set-the-method-in-thresholdimagefilter-in-sitk/4053)

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**Author:** [@Floowey](https://discourse.itk.org/u/Floowey)\
**Replies:** 2\
**Last updated:** [April 20, 2021, 5:18pm UTC](https://discourse.itk.org/t/how-to-set-the-method-in-thresholdimagefilter-in-sitk/4053 "2021-04-20T17:18:19Z")

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Hello, I’m trying to work my way around the ThresholdImageFilter class. My goal is to “cap” the image at some lower and upper bound (lb, ub). Everything below lb shall be set to lb and everything above ub shall be set t…

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## [method "GetLogBiasFieldAsImage" missing in N4BiasFieldCorrection c# implementation](https://discourse.itk.org/t/method-getlogbiasfieldasimage-missing-in-n4biasfieldcorrection-c-implementation/4033)

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**Author:** [@Tamar](https://discourse.itk.org/u/Tamar)\
**Replies:** 5\
**Last updated:** [April 20, 2021, 1:47pm UTC](https://discourse.itk.org/t/method-getlogbiasfieldasimage-missing-in-n4biasfieldcorrection-c-implementation/4033 "2021-04-20T13:47:49Z")

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Hello, I have the N4BiasFieldCorrectionImageFilter implemented in c# (visual studio) and it is working correctly and improving images. However, when I attempt to use the method GetLogBiasFieldAsImage() I get the follo…

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## [Build ITKPython module with additional supported data types](https://discourse.itk.org/t/build-itkpython-module-with-additional-supported-data-types/4042)

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**Author:** [@Alex\_Reimelt](https://discourse.itk.org/u/Alex_Reimelt)\
**Replies:** 6\
**Last updated:** [April 20, 2021, 9:01am UTC](https://discourse.itk.org/t/build-itkpython-module-with-additional-supported-data-types/4042 "2021-04-20T09:01:59Z")

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Dear ITK community, after generating radially distorted images of lung tissue for my PhD project with ITKPython, I have realized that multiple filters I use do not support certain ITK data types. In order to solve this …

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## [How to get the window width and window level of DICOM file, and set VR data to display only bones according to the window width and window level.](https://discourse.itk.org/t/how-to-get-the-window-width-and-window-level-of-dicom-file-and-set-vr-data-to-display-only-bones-according-to-the-window-width-and-window-level/4045)

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**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 1\
**Last updated:** [April 19, 2021, 1:38pm UTC](https://discourse.itk.org/t/how-to-get-the-window-width-and-window-level-of-dicom-file-and-set-vr-data-to-display-only-bones-according-to-the-window-width-and-window-level/4045 "2021-04-19T13:38:23Z")

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How to get the window width and window level of DICOM file, and set VR data to display only bones according to the window width and window level.

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## [Issue with reading mhd image file](https://discourse.itk.org/t/issue-with-reading-mhd-image-file/4038)

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**Author:** [@spb](https://discourse.itk.org/u/spb)\
**Replies:** 4\
**Last updated:** [April 17, 2021, 6:28am UTC](https://discourse.itk.org/t/issue-with-reading-mhd-image-file/4038 "2021-04-17T06:28:19Z")

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Hi, I am reading mhd image file in python using SimpleITK as follows. sitkimage = sitk.ReadImage(mhdFile) The issue is, after reading image, size is changed. Original Image (width, height, depth) → (1024, 512, 128) …

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## [How to upsample two coregistered images ?](https://discourse.itk.org/t/how-to-upsample-two-coregistered-images/4025)

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**Author:** [@Hugo](https://discourse.itk.org/u/Hugo)\
**Replies:** 10\
**Last updated:** [April 15, 2021, 12:51pm UTC](https://discourse.itk.org/t/how-to-upsample-two-coregistered-images/4025 "2021-04-15T12:51:10Z")

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Hello, I have two images 1 PET and 1 MRI that are perfectly aligned (they are acquired simultaneously). MRI shape is (512, 512, 1312) PET shape is (192, 192, 566) I would like to upsample the PET image so it matches …

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