05 Basic Registration tutorial error

Beginner Questions
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1

Hello,

I’m following the SimpeITK MICCAI tutorial (2020), and I can’t reproduce the results in the Initialisation section of the notebook 05_basic_registration, because I get the following error:

AttributeError: module ‘SimpleITK’ has no attribute ‘ImageSeriesReader_GetGDCMSeriesFileNames’

I have checked and all the dependencies are installed. I have used pip to install most of them and I’m running on anaconda. Do you have any idea of what can be causing this error? Many thanks

2

Hello @Priscilla,

This is a strange error, the function has been available without change in SimpleITK from very early versions.

Is there a specific reason you are using anaconda Python and installing packages via pip? The guidance in the tutorial is to use anaconda and create the virtual environment via:

conda env create -f TUTORIAL/environment.yml

Before we attempt to debug any further, please follow the tutorial’s setup instructions and see if using that virtual environment solves the issue. If not, then please provide more details on your configuration: OS, Python version, SimpleITK version.

3

Hi Ziv,

Thank you very much for your quick response.

I did actually create a virtual environment in anaconda to install sipleITK. However, I found that some ITK dependencies were unavailable through conda and had to use pip to install them instead. In any case, I will double-check all the installation steps and let you know if it works.

Regards,

Priscilla

4

Hi Ziv,

I reinstalled the tutorial using the terminal, instead of the anaconda navigator, and all seems to work now :slight_smile:

Regards,

Priscilla

5

Good luck with the rest of your image analysis journey, :rocket: .