Result of non-rigid registration / ImportError: No module named '_SimpleITK' /

[samieti02]

Hello dear Sir or Madam, thanks for the tool. I would like to mention a few points and a few questions I would have too. I spent a lot of time getting the tool up and running. After that, I tried a non-rigid registration and those are the results I had.

• Could you please explain why you have this light box around the skull (Image Regof12)?

• I find that the documentation is not well described. for example you said for linux, we should use git clone https://github.com/SuperElastix/SimpleElastix and for windows git clone https://github.com/kaspermarstal/SimpleElastix What is the different between both ? I have Windows 10 64 bit with VS 2015. I installed anaconda 3 and the latest version of cmake. I first tried with the second link for windows and always had compile errors, then i tried with the first link, and everything was Ok; i should also mention that i made some changes within cmake and VS2015. The build was successful and i was of course happy.

• Then i tried the first simple code and immediately the next error comes up (datapre) C:\Users\me\Datapre>cd c:\Users\me\Datapre && cmd /C "set "PYTHONIOENCODING=UTF-8" && set "PYTHONUNBUFFERED=1" && C:\Users\me\AppData\Local\Continuum\anaconda3\envs\datapre\python.exe c:\Users\me\.vscode\extensions\ms-python.python-2018.6.0\pythonFiles\PythonTools\visualstudio_py_launcher_nodebug.py c:\Users\me\Datapre 58302 34806ad9-833a-4524-8cd6-18ca4aa74f14 RedirectOutput,RedirectOutput c:\Users\me\Datapre\datapre.py " Traceback (most recent call last): File "c:\Users\me\.vscode\extensions\ms-python.python-2018.6.0\pythonFiles\PythonTools\visualstudio_py_launcher_nodebug.py", line 74, in run _vspu.exec_file(file, globals_obj) File "c:\Users\me\.vscode\extensions\ms-python.python-2018.6.0\pythonFiles\PythonTools\visualstudio_py_util.py", line 119, in exec_file exec_code(code, file, global_variables) File "c:\Users\me\.vscode\extensions\ms-python.python-2018.6.0\pythonFiles\PythonTools\visualstudio_py_util.py", line 95, in exec_code exec(code_obj, global_variables) File "c:\Users\me\Datapre\datapre.py", line 17, in <module> import SimpleITK as sitk File "C:\Users\me\AppData\Local\Continuum\anaconda3\envs\datapre\lib\site-packages\simpleitk-1.0.1rc1.dev345+g9dfa8-py3.4-win-amd64.egg\SimpleITK\__init__.py", line 1, in <module> from .SimpleITK import * File "C:\Users\me\AppData\Local\Continuum\anaconda3\envs\datapre\lib\site-packages\simpleitk-1.0.1rc1.dev345+g9dfa8-py3.4-win-amd64.egg\SimpleITK\SimpleITK.py", line 17, in <module> _SimpleITK = swig_import_helper() File "C:\Users\me\AppData\Local\Continuum\anaconda3\envs\datapre\lib\site-packages\simpleitk-1.0.1rc1.dev345+g9dfa8-py3.4-win-amd64.egg\SimpleITK\SimpleITK.py", line 16, in swig_import_helper return importlib.import_module('_SimpleITK') File "C:\Users\me\AppData\Local\Continuum\anaconda3\envs\datapre\lib\importlib\__init__.py", line 109, in import_module return _bootstrap._gcd_import(name[level:], package, level) ImportError: No module named '_SimpleITK'

It was really annoying, cause i passed a lot of time with the build. I dowloaded the wheel data from the internet page and installed it,

Installed c:\users\me\appdata\local\continuum\anaconda3\envs\datapre\lib\site-packages\simpleitk-1.0.1rc1.dev345+g9dfa8-py3.4-win-amd64.egg Processing dependencies for SimpleITK==1.0.1rc1.dev345+g9dfa8 Finished processing dependencies for SimpleITK==1.0.1rc1.dev345+g9dfa8

and everything was ok. I would say that I was a bit lucky. The documentation also helped, but I'm not completely satisfied. I would like to know if the process I took to install it, is reasonable?

Thanks and Regards Sami

[samieti02]

Hello dear people, could i have please a feedback? Why do i get a box around the skull? Which parameter should I use to optimize the results? The number of iterations didnt help. Which do you have? Thanks

[PertuyF]

It is not a "box", it is the background of your image that does not appear black.

Most likely your pixeltype changed during the registration (guessing from int16, somewhat standard for medical imaging, to float32, the default for ElastiX output) which modified the dynamic range of your image, and your viewer does not adjust. Changing the contrast inside your viewer should make the background appear "black" again.

[samieti02]

thks for the (1) reply !

[kaspermarstal]

You are not the first user to come across the "No module" error. I don't know the cause at the moment, but working on a fix.

[kaspermarstal]

Run sudo python Packaging/setup.py install from the Wrapping/Python directory, not sudo python setup.py install from the Wrapping/Python/Packaging directory