Image segmentation and registration using SimpleITK

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image segmentation simpleitk
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simpleitk dicom

I have some doubts regarding 3D image registration and segmentation:

  1. 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

  2. Registration: registration is pretty straight forward, we have to register all 100 stacks to the first stack.

  3. Registration accuracy : SimpleITK overlap ratio measure or hausdroff distance need segmentation and labelling. Now segmentation using region growing or thresholding is not easy for all kind of images. Let suppose I just want to select a region manually , interactively. Is it possible to achieve that ? Then I just want to use that selected mask for registration accuracy evaluation.

  4. Visualization and write : need to visualize in 3D using matplotlib or VTK. All plot functions are working for 2d slice, again visualizing in 2D is not desired. While writing to a dicom image using simpleITK write Image function, for dicom image just writing the image object is not working. We need to change type to UInt32 , but then the image becomes lossy. It successfully writes to a .mha format, but imageJ fails to display.

If possible please share your thoughts.

I am not sure whether SimpleITK supports 4D images in its default configuration. If not, you would have to compile it yourself, after having it configured to support dimension 4 (and not just 2 and 3). Even with that, I am not sure it would work right away - DICOM is notorious making simple things not so easy, and complicated things super-hard.

ITK-SNAP is a tool for manual and manually assisted segmentation.

Visualization is more a VTK question. Here is an example which uses 3D visualization.

I am not sure whether SimpleITK supports 4D images in its default configuration. If not, you would have to compile it yourself, after having it  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: registration is pretty straight forward, we have to register all 100 stacks to the first stack.

1) GetImageFromArray, simpleITK in python> convert a 4d numpy array to a SimpleITK image.

import numpy as np
import SimpleITK as sitk

np_array = np.zeros( (a,b,c,d) )
tdim = np_array.shape[3]
slices = []

for i in range(tdim):
    slices.append( sitk.GetImageFromArray( np_array[i], False ) )

im = sitk.JoinSeries(slices)

sitk.WriteImage(im, "imageresult.mha") 

2) You can first select you VOI using ITKsnap, or in your python code and instead of performing all your experiments on the whole image data, you can only include that ROI.

3) use> from myshow import myshow

myshow(sitk.LabelToRGB(img), title='img')

2018 Aug;86. pii: 8. doi: 10.18637/jss.v086.i08. Epub 2018 Sep 4. Image Segmentation, Registration and Characterization in R with SimpleITK. Beare R(1)​  SimpleITK is a simplified interface to the insight segmentation and registration toolkit (ITK). ITK is an open source C++ toolkit that has been actively developed over the past 18 years and is

3D Slicer has functionality to load DCE MRI series as 4D volumes. You can find the tutorial how to use this functionality of 3D Slicer in this post: https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622.

Developed by the Insight Toolkit community for the biomedical sciences and beyond. Registration framework for fast alignment of 2D and 3D intra and An abundance of filters for image segmentation workflows, from classics such as Otsu  SimpleITK is a simplified interface to the insight segmentation and registration toolkit (ITK). ITK is an open source C++ toolkit that has been actively developed over the past 18 years and is widely used by the medical image analysis community.

In this course, we will use a hands-on approach utilizing Python based SimpleITK We then turn our focus to the toolkit's registration framework, exploring various an image analysis workflow that includes segmentation and shape analysis. General introduction of SimpleITK on the International Society for Computer Aided Surgery blog, 1 March 2017. SimpleITK and R, 22 May 2015. Medical Image Analysis Course, 20 December 2014. Image Segmentation with Python and SimpleITK, October/November 2014. Support. SimpleITK is supported through the ITK community and the active developers.

C++ library with wrappers for Python, Java, CSharp, R, Tcl and Ruby based tutorial on the use of the ITKv4 registration framework via SimpleITK. Image Segmentation with Python and SimpleITK, October/November 2014. SimpleITK is a simplified programming interface to the algorithms and data structures of the Insight Segmentation and Registration Toolkit (ITK). It supports bindings for multiple programming languages including C++, Python, R, Java, C#, Lua, Ruby and TCL.

It includes a whole bunch of goodies including routines for the segmentation, registration, and interpolation of multi-dimensional image data. Just  Image registration with SimpleITK. Ask Question Asked 2 years, 4 months ago. Image segmentation and registration using SimpleITK. 2. SimpleITK Resize images. 1.