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Questions tagged [simpleitk]

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.

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How do I use SimpleITK's ExpandImageFilter?

I have 2 SimpleITK images, and I want to use their package's ExpandImageFilter to upsample one of my images to match the other. Does anyone have any idea on how to use this? I took a look at their documentation…
Icy Lemons
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SimpleITK read io.ByteIO

I have a io.ByteIO object which represent an uploaded image (.nii), is there a way to obtain an simpleITK object from it ? A bad workaround would be to write the file then read it with simpleITK
Chopin
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Convert Dicom image pixel value to Unity color

I use SimpleITK to read a Dicom image in Unity. I create a list of Unity Texture2D to store Dicom slices. My question is how can we convert the pixel value from Dicom image to Unity Color? List _imageListTexture = new…
vuthea
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Check file before calling SimpleITK.SimpleITK.ImageFileReader.ReadImageInformation()

I am processing a set of DICOM files, some of which have image information and some of which don't. If a file has image information, the following code works fine. file_reader =…
OtagoHarbour
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Limiting DICOM tags

I am trying to limit the DICOM tags, which are retained, by using for key in keys: if key.upper() not in {'0028|0010','0028|0011'}: image_slice.EraseMetaData(key) in Python 3.6 where image_slice is of type SimpleITK.SimpleITK.Image I…
OtagoHarbour
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Python: update plot with image with slider weight

I loaded a .nii file in my application. def show(self): image = SimpleITK.ReadImage(file_name) t1 = SimpleITK.GetArrayFromImage(image) t2 = color.rgb2gray(t1[w.get()]) print(w.get()) print(t2.shape) plt.ion() fig =…
Cristina Bîrsan
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SimpleITK for image registration. Writing issue

I've installed from sources the SimpleITK package on Python3. When I perform the provided registration example : #!/usr/bin/env python #========================================================================= # # Copyright NumFOCUS # # …
ananass
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How to save an array with the same spacing and origin into a SimpleITK image?

I want to write the image [that I have loaded into array] after changing the values of array into a SimpleITK Image. How can I set the spacing and origin? [res_file_dir is the path to the nii.gz…
S.EB
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How to use SimpleITK "LabelOverlapMeasuresImageFilter" to extract measures on Python using NiftiImages

I need to extract a set of metrics from 2 labeled 3d images, with the same dimensions, data types EVERYTHING IS THE SAME, except that one is my silver standard and the other one is the result of a pipeline. my code is: reader =…
Vitor Hugo
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Assignment to indexed images in SimpleITK

What is the best way to do assign values or slices to indexed arrays in SimpleITK? Example (1): Assigning a 2D slice to an indexed 2D slice in a 3D volume In NumPy, we can do the following assignment to the index arrays: import numpy as np nda =…
mehrtash
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SimpleItk crop image

I would like to crop a 3D image using simpleItk in Python3 first, loading the image and get numpy array image_ct = sitk.ReadImage(path_ct, sitk.sitkInt16) array_ct = sitk.GetArrayFromImage(image_ct) then I do a crop on array data center = (200,…
Chopin
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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 to access specific voxels that satisfies the specific condition in ITK C++?

I have a 3D image and a sphere equation. I need to take out all the voxels that are outside the circle and want to apply a transformation to them. How do I differentiate those points from all the points? I'm not understanding how to actually write…
Cndu
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BSplineTransform.GetInverse() throws sitk::ERROR: Unable to create inverse

I calculated a B-spline transform in Python using the method described in the docs, and trying to invert it using bspline.GetInverse(). This causes the following error: Traceback (most recent call last): ... File…
Michael Litvin
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