SimpleITK is a simplified, open-source interface to the United States National Library of Medicine’s Insight Segmentation and Registration Toolkit. The SimpleITK image analysis library is available in multiple programming languages including C++, Python, R, Java, C#, Lua, Ruby and Tcl.
Questions tagged [simpleitk]
221 questions
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1 answer
Can not "link"SimpleITK::Show() with FIJI
I am running on Ubuntu. When calling the Show method of SimpleITK I am not being able to view such image in my FIJI ( ImageJ2) window.
Given that FIJI is a portable application, is it necessary to perform some more process in order to properly link…
Francisco Cunha
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1 answer
Image Registration accuracy evaluation (Hausdroff distance) using SimpleITK without segmenting the image
I have registered two images, let's say fixed and moving are Registered. After registration I want to measure overlap ratio etc.
The SimpleITK has overlap measure filters and to use overlap_measures_filter.Execute(fixed, moving) and…
Subhajit
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2 answers
How to implement model-to-image registration in SimpleITK?
I installed SimpleITK for medical image registration. It works very well for 3D CT/CT and 3D CT/MRI image registration. Now I want to implement model/image registration. The model is a sphere. In ITK there are Spatial Objects like Box, Ellipse which…
David Lau
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2 answers
How to extract labels from a Binary Image in SimpleITK in python
I would like to extract the labels from the 2D Binary image I get using the following code:
image2DThresh = sitk.Threshold(image2D, lower=stats.GetMinimum(), upper=127.500)
cca = sitk.ConnectedComponentImageFilter()
cca_image =…
Rick M.
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2 answers
How to use SimpleElastix as a reference of a new C# project?
I git clone SimpleElastix [1] project from https://github.com/kaspermarstal/SimpleElastix, and built and compiled it successfully on my PC. The WRAP_CSHARP option was set in CMAKE. I would like to use this project as a reference/framework to…
Siming
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1
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2 answers
simpleITK with anaconda python
I am trying to install simpleITK on my macbook which has mavericks running on it. I have installed Anaconda python.
When I try to import SimpleITK as sitk, I get the following error
import SimpleITK as sitk
Traceback (most recent call last):
…
user2441416
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2 answers
Display a Simpleitk image in a picture Box
I want to read a dicom or png image with simpleitk in a C# program and display the result in a pictureBox. I understand that picture Box allow only "system.drawing.image" and not itk. Is there a way to do it.
Her is my code :
OpenFileDialog fd =…
user2827482
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1 answer
How to decide the value of the sigma value to use for the SimpleITK Filter: SmoothingRecursiveGaussianImageFilter depending on the voxel size?
I am using a code similar to this example in order to smooth voxel volume data (so from a CTA scan): https://examples.itk.org/src/filtering/smoothing/computessmoothingwithgaussiankernel/documentation
and wondering, what sigma value to use? Does it…
Alex1111
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Simple ITK slicing on coronal direction ends up with an upside down image?
SimpleITK version '2.2.0'.
Python version 3.9.3
Numpy version 1.24.2
I was using SimpleITK to read in an image and then slicing it on different direction. For example, the image is 'image.mhd', I read it in as:
image =…
user1836485
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The execution of SimpleITK's STAPLE algorithm gets stuck in certain cases
I am running the STAPLE algorithm to ensemble 9 segmentations from several models (each segmentation has 3 labels (1,2,3) and the background (0)), but it is getting stuck in some cases (specifically 2 cases). I wonder if someone is having the same…
Andre Ferreira
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0 answers
SimplyITK Size must be specified when trying to run N4BiasFieldCorrection
I am working on trying to get this function working in python, but i get Size must be specified error.
# if input img is numpy array convert to sitk Image
try:
img_in = sitk.GetImageFromArray(img)
except:
img_in = img
#…
JRowan
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Change Direction of an image to match a reference, and obtain Origin, without changing the original voxel spacing
I apologize and thank you Ori I will have to edit my question since I wasn't so clear. What I try to do is to calculate the new origin for new direction. The images belong to the same patient, same study, T2 and ADC.
import SimpleITK as…
HarryKa
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SimpleITK copy headers/metadata to align segmentation with image
I am trying to copy all the metadata/header information from one image to another.
I have a segmentation (original_image) that when I overlap it with the MRI image it comes from it overlaps as expected (comparing it in 3D Slicer, for instance). I…
0
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2 answers
Where do i get SimpleITK JNI Lib?
using intellij in windows and i'm getting this error: java.lang.UnsatisfiedLinkError: no SimpleITKJava in java.library.path
reading this tutorial: https://itk.org/Wiki/SimpleITK/GettingStarted/A_visual_guide_to_SimpleITK_in_Java
i find a…
Salu Ramos
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0 answers
no SimpleITKJava in java.library.path with intellij
i am trying to use simpleitk with java.
already setup pom.xml and maven works with no error or warning.
i can even import simpleitk in my scripts and run without problems.
when trying to make something a little bit more complex, i bumped…
Salu Ramos
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