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Questions tagged [elastix-itk]

Elastix is a toolbox for rigid and nonrigid registration of images based on ITK. Not to be confused with the Elastix Unified Communication Server.

Elastix is a toolbox for rigid and nonrigid registration of images based on the well-known Insight Segmentation and Registration Toolkit (ITK).

It is a open source collection of algorithms commonly used to solve medical image registration problems. Elastix has a command-line interface for processing of large numbers of data sets. It can also be used with C++, Python, Java, R, Ruby, Octave, C#, and Lua via SimpleElastix, an extension to SimpleITK.

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How to get transformation affine from ITK registration?

Given 3D MRI scans A, B, and C I want to perform an affine (co)registration of B onto A, take the transformation affine matrix of the registration and apply it on C. My problem is that the affine matrix of the registration transform has the wrong…
Spenhouet
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Issues Installing SimpleElastix on Ubuntu for Python

I am trying to install SimpleElastix/SimpleITK on an Ubuntu computer for either Python2 or 3, whichever we can get to work. Using pip install doesn't work as various methods don't import then (e.g. no "GetDefaultParameterMethod" exists). I tried…
cmitch
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How can I perform 3d image registration using SimpleElastix from Python?

I'm trying to register two 3d volumes. An attempt at this can found here. The code first generates two different volumes, both containing exactly one sphere of radius 4. I'm then trying to align them using the default translation parameter map.…
Rule
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Use CMAES optimizer in Elastix, How to define class TElastix?

I'm trying to write my own registration method by using iTk and elastix, I do have some experience in iTk but I just started to use its extension called Elastix. I want to use CMAES optimizer in elastix to find the optimized values of translation…
Ramyar
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Simple ITK Problem when saving deformation field : the deformation field is empty

I'm looking for help with simpleITK, I'm working with NII files in order to calculate the deformation field. I use Python and simpleITK (simpleitk 1.2.0rc2.dev1167+gd4cf2). I can easily register my images or volumes but I cannot get the deformation…
Armand
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Install SimpleElastix on Windows for Python

It seems some people have reported this on GitHub but I still couldn't find a clear solution to it - in the last step of installing the python module on Windows, there is no such folder called "/Wrapping/Python/Packaging" under "SimpleITK-build",…
Linghua
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How can you reuse ImagePyramids in SimpleElastix?

I am using SimpleElastix to perform image registration. I am trying to align different images (aka moving images) to the same template (fixed image). One of the slowest parts is Preparation of the image pyramids. How can I speed it up ? I was…
Ciprian Tomoiagă
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SimpleITK::ERROR: Error in administrating child process: [No such file or directory]

My Python Code is: import SimpleITK as sitk resultImage = sitk.Elastix(sitk.ReadImage("fixedImage.nii"), \ sitk.ReadImage("movingImage.nii"), \ "translation") sitk.Show(resultImage, 'test',…
dieKoderin
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Elastix 3D registration stops python without any error

I want to register 2 3D datasets that are read into numpy arrays and then given to the registrate() function. When I execute the code it prints the following log: Installing all components. InstallingComponents was successful. ELASTIX version:…
Kai Winkler
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Manual registration with SimpleElastix

I'm using SimpleElastix (https://simpleelastix.github.io/) for the registration (Affine) of the two 2D images (see attached) . For this I'm using this code : import SimpleITK as sitk elastixImageFilter =…
jeanluc
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Simple ITK Elastix installation on Windows 10 from Sources with CMake to run in Python

I have to try to install SimpleITK Elastix on Windows 10. I have the toolchain (Windows 10, Anaconda3, python 3.7 , MSVS 2019, Cmake 3.7, git,) and source code (SimpleITK v1.2, SimpleElastix KIT). It do all steps all right but after run python setup…
candido
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How to determine if client or agent hung up?

I have an elastix server4, but I have a big problem. I don't know how to find who hung up the call (agent or client). How do I determine if client or agent hung up?
MLazar
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