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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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Image registration with SimpleITK

I want to do multi-modality image registration(mri/ct) but I do not have completely aligned images, results obtained with simpleITK are very bad. Even if I try to align them, results are still ridiculously bad. What can I do to fix this? My…
Willy Sun
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How to use SimpleITK.WarpImageFilter function in python

I can't find any python documentation on this function. I tried the following code, but the output is absolutely wrong. warp = sitk.WarpImageFilter() warp.SetInterpolator(sitk.sitkLinear) out = warp.Execute(reference_img, transform_img) it gives me…
Yang Li
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Convert mha 3d images into 2d images in Python (2015 brats challenge dataset)

I want to use SimpleITK or wedpy to convert the 3d images into 2d images. Or i want to get a three-dimensional matrix, and then i divide the three-dimensional matrix into some two-dimensional matrices. import SimpleITK as ITK import numpy as…
hey6775
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how to use simpleitk get inverse displacement field

I just moved from matlab to python recently so I can use simpleitk and sorry if this is a dumb question. I have a transformation tx after demons registration using simpleitk. I wish to get the displacement field and its inverse by doing the…
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Siemens CT dose report/patient protocol PixelData

I’m trying to extract dicom PixelData from Siemens’ dose report but it contains only zeros. With GE dose report I read the data without a trouble with pydicom or simpleITK. Any ideas why siemens report contains only zeros? Thanks! Came this far, but…
davidx300
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Not able to write image SimpleElastix (Python)

I'm trying to run the following example as part of the SimpleElastix library: import SimpleITK as sitk elastixImageFilter = sitk.ElastixImageFilter() elastixImageFilter.SetFixedImage(sitk.ReadImage('1.jpg',…
Simplicity
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Using Simple ITK to find bounding box

How can I capture the bounding box from the 3D mask by using Simple ITK in python? The ITK has the bounding box function, but I couldn't find similar function in SITK.
Hamid
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error: could not convert string to float (CordZ)

I am trying to extract nodule patches from CT images based on the co-ordinates given in a CSV file. i keep getting this error msg at the worldcoord line :could not convert string to float(CordZ). I am not quite sure how to do that. I have this so…
Anil Yadav
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Transform object has no attribute GetInverseTransform

This is not a duplicate, please take the few seconds it'll take to read my question, I would be glad. I'm currently using the RegistrationMethodClass from simpleITK registration. Due to there being a lot of noise in the fixed image (which could…
Alceste_
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SimpleITK python 2.7.12 installation issue

So... I'm trying to install SimpleITK on Python 2.7.12 and I tried several ways which none is giving me satisfatory result. 1) by simply using pip install SimpleITK I get "No matching distribution found for SimpleITK" (my pip version is 9.0.1) 2)…
user
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Can python sitk.ReadImage read a list/series of images?

I do not understand if sitk.ReadImage can read a list of images or not? I did not manage to find an example showing how to list of images should be inputed to the function. But in the function documentations it say: ReadImage(**VectorString…
Oren
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How do I install SimpleITK on macOS for Anaconda Python 3.6?

import setuptools easy_install SimpleITK-0.8.0.post48-py2.7-macosx-10.5-x86_64.egg I downloaded the .egg file and tried using easy_install but it doesn't seem to be working. This is the error I am getting. easy_install…
Ilan
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simpleITK N4BiasFieldCorrection performs strange in terms of running speed and results

I am doing a project about brain tumor segmentation. And when I apply N4BiasCorrection to my file(.mha), I used slicer and simpleITK methods. Slicer performs well but is time-consuming because I do not know how to use code to run through all my…
Chen
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Image segmentation and registration using SimpleITK

I have some doubts regarding 3D image registration and segmentation: Load dicom images: In DCE-MRI there are 4000 slices and total 100 stacks, so 40 in each stack. How can I load them to a 4D array using GDCM simpleITK function Registration:…
Subhajit
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SimpleITK linking from Visual Studio 2008

This is a question for anyone using SimpleITK from within a C++ program. I have downloaded the SimpleITK code, and generated the VS2008 .sln files using CMake as per SimpleITK instructions (Superbuild). In the SimpleITK-build\lib\Debug I get a few…
BeMeCollective
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