simpleitk

sudo easy_install for SimpleITK not that easy

由 為{幸葍}努か 提交于 2019-12-13 15:25:35
问题 So... I've tried several ways to download SimpleITK (pip install) on Python but it's not working at all! (Here: SimpleITK python 2.7.12 installation issue) Now I'm using easy_install and I get this error: Searching for simpleitk Reading https://pypi.python.org/simple/simpleitk/ Download error on https://pypi.python.org/simple/simpleitk/: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:590) -- Some packages may not be found! Couldn't find index page for 'simpleitk' (maybe

Image segmentation and registration using SimpleITK

由 谁说胖子不能爱 提交于 2019-12-12 04:28:58
问题 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. Registration accuracy : SimpleITK overlap ratio measure or hausdroff distance need segmentation and labelling. Now segmentation using region growing or

SimpleITK python 2.7.12 installation issue

由 青春壹個敷衍的年華 提交于 2019-12-12 04:12:32
问题 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) tar file (available here: https://sourceforge.net/projects/simpleitk/files/SimpleITK/1.0.0/Python/): when I run the command python setup.py install I get: Download error on https://pypi.python.org/simple/scikit-build/: [SSL: CERTIFICATE_VERIFY_FAILED

Python - Write a three dimensional image from 3D array

由 落花浮王杯 提交于 2019-12-11 04:48:46
问题 I'm trying to obtain an image from 3D array and convert it to TIF 3D. I'm using simple ITK but it doesn't work. I obtain this error message : 'in method 'WriteImage', argument 1 of type 'itk::simple::Image const &' Here's my code: import numpy as np import SimpleITK as sitk test = np.ones((20,20,20)) sitk.WriteImage(test,'test.tif') -------------------- EDIT LATER ---------------------------- I try by working with "GetImageFromArray" it seems work as i keep the same size and finally i try to

Where can I find the SimpleITK documentation and reference information?

由 荒凉一梦 提交于 2019-12-04 11:55:13
问题 I am interested in trying to use SimpleITK to solve my imaging problem. Can you please tell me where the documentation and training materials are? 回答1: SimpleITK is documented here, and has a tutorial that has been presented at the MICCAI 2011 conference. Development of SimpleITK is hosted on Github and feature requests can be entered in Jira. Direct Links: https://github.com/SimpleITK/SimpleITK-MICCAI-2011-Tutorial https://github.com/SimpleITK/SimpleITK http://www.simpleitk.org 回答2: There

How are the spacing value of the z dimension and thickness (0018, 0050) different in dicom series?

由 会有一股神秘感。 提交于 2019-12-01 11:08:31
I've been studying some dicom series and find that the thickness attribute and the itkimage.GetSpacing()[2] value are not always consistent. For example the thickness (0018, 0050) value encoded in the dcm file is 1.5 mm but the corresponding spacing indicated simpleITK on z axis is 1.00 . Then what value should I use to indicate the physical distance between adjacent voxel center s on the z axis? If they are different things then What do spacings actually mean? I retrieve thickness and spacing values in python like this: //thickness using dicom thickness = dicom.read_file(dcm_file)[0x0018,
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