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
0
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1 answer
Getbuffer method in SimpleITK libraries to read an image and output another
Here there,
I'm currently working on a C# project and I need to create a snippet using SimpleITK libraries, in which my image matrix ArrayIn will be compared to a number DoubleVar.
Then, if, for each element, the value of ArrayIn is greater than the…
user3213352
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1 answer
how to get an axial image from ct scan images. as i am using sliver07 dataset so it has 100+ images in single .mhd file
i using SLIVER07 dataset for liver segmentation task but i am stuck in reading that images.
import SimpleITK as sitk
import numpy as np
import matplotlib.pyplot as plt
# reading .mhd file from slive07 dataset
itkimage =…
Qazi Sami Ullah Khan
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- 2
-1
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1 answer
Registering a pair of binary masks
I'm trying to register a pair of binary masks, not a pair of images.
To explain further, I'm trying to build a model that automatically strips the brain from the head skull. For the better model accuracy, I already have labeled the brain area using…
goofyduck
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- 2
-1
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1 answer
From numpy array to a mhd file in python
I'm trying to convert a numpy array into a mhd file using SimpleITK.
Do you know if this is possible and if so, how to do it ?
manon
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-1
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1 answer
How to integrate SimpleITK in Unity for app in HoloLens 2
I'm developing an app in Unity 2020.3.3f1 to be deployed in HoloLens 2. This app has to deal with medical images thus I need to use SimpleITK library.
I've downloaded SimpleITK source files and compiled them in Visual Studio 2017 for ARM64…
Elena Stocco
- 11
- 2
-1
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1 answer
SimpleItk - writing a DICOM image using 12 bits (BitsAllocated=16, BitsStored=12)
I have an original DICOM file that has DICOM tags BitsAllocated (0028|0100)=16 and BitsStored (0028|0101)=12. I use SimpleITK to read this series, modify it and then I would like to save it again as a DICOM series using the same values for the two…
F.Lotte
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1 answer
How to change only array for Dicom file with Simple ITK in python
I have a bunch of medical images in dicom that I want to correct for bias field inhomogeneity using SimpleITK in Python. The workflow is straightforward: I want to (1) open the dicom image, (2) create a binary mask of the object in the image, (3)…
fednem
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- 13
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1 answer
Change of coordinates under resampling operation in itk
If i have a large image and i resample it to a smaller size. How can i apply the same transformation to the coordinates in the larger image. Specifically, if I resample an image to a smaller size, what are the new coordinates of the points in the…
arrhhh
- 99
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- 16
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1 answer
Why I get a very low negative Entropy for all my dataset?
I am doing first order statistics for selected regions from a series of different images. I am using Pyradiomics package to calculate Kurtosis and Entropy, The problem is that I always get the same very low value for the entropy…
Omar Kamal
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1 answer
simpleitk installation in anaconda
i installed simpleitk in anaconda using command
conda install -c simpleitk simpleitk then followed link https://github.com/SimpleITK/SimpleITKCondaRecipe to build it but it's not connecting to itk.org to build.
import SimpleITK as sitk on jupyter…
anita dhawan
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