Issues for Notebooks - Training 3

[CobbleVision]

Dear Ozan-Oktay,

I attempted to revive your Medical-Image-Analysis Notebooks (Training 3) and ran into several issues. Perhaps you can help me out or provide some hints on where to look at for resolving these.

1. One of the first hurdles was to setup the environment in conformant mode to the scripts. Some of the packages are rather old by now and do not support certain functions anymore. e.g. GMM's are now different and newer implementations do not support "thresh" args.

2. I could only get otsu_tresh.ipynb to work properly. The other notebooks ran into issues along the way. Some of these are in data transformations, mathematical operations or splicing, to which I am unsure on how to resolve. For example atlas_priors failed in result visualization during splice for me, which makes results not visualizable. Exporting an image instead of looking at the spliced presentation resulted in a black png, although the graph looks calculated correctly.

3. The em_seg.ipynb notebook failed completely for me due to dimensional errors in handling the input images and forwarding them into the GMM.

Here is the setup, which I finally used to test the notebooks, which I converted into Python Files manually:

• Python 3.5 environment using anaconda
• conda install scipy==0.19.1 scikit-learn=0.19.0 VTK matplotlib
• pip install SimpleITK vtk-python==5.8.0

I am really interested in your notebooks, as I'd like to upload your code to cobblevision.com, which is a marketplace and SaaS for computer vision. If you could it to work, you can also upload your work there, and make your code executable for others without writing any code! Otherwise I'll do it once everything is working again!

Best regards,
Cob