Assignment 3: SimpleITK Notebooks
Methods In Medical Image Analysis (BioE 2630 : 16-725) - Spring 2017

Creative Commons License SimpleITK Notebooks 1 assignment by John Galeotti, © 2017 Carnegie Mellon University, is licensed under a Creative Commons Attribution 3.0 Unported License. Permissions beyond the scope of this license may be available by sending email to itk ATgaleotti.net. (The SimpleITK Notebooks referenced are separately © by their own authors, etc..)

Please contact Dr. Galeotti with any questions: galeotti+mimia_nb1 ATcs.cmu.edu

15 points total

Due Date: Email your submission to Dr. Galeotti by 5pm on Tuesday night, Feb. 28.

You should have previously downloaded a set of SimpleITK notebooks by using git as instructed in assignment 2.4. You should now open a command prompt and change to your SimpleITK-Notebooks folder before launching iPython's notebook interface:

cd \miia\SimpleITK-Notebooks
jupyter notebook

Submit everything as a single email.

(Windows users can install the free and open source PDFCreator to print to pdf. Macs can natively print to pdf files.)

Problem 1  4 points)

Open and work through the first part of notebook 300_Segmentation_Overview.ipynb, but stop when you get to the fast-marching level set. When finished, "print"/save the entire completed portion (up until level sets) of the notebook as a pdf file. Email the pdf to your grader/instructor.

Problem 2  (4 points)

Open and work through all of 30_Segmentation_Region_Growing.ipynb. After completing this notebook, "print"/save the entire notebook as a pdf file. Email the pdf to your grader/instructor.

Problem 3  (7 points)

Finally, include in your email (not as an attachment) a 100-200 word description of the differences between all the threshold-based altorighms you just used, including your observations as to their strengths, weaknesses, and best applications for use.

 

Future assignment:

Make students use SNAP now. Show them how to load an image and an expert segmentation, and then compare both with their own segmentaiton. Mention that because (Simple)ITK is for programmers it starts numbering at 0, but ITK-Snap was made for "clinicians" and so starts numbering at 1. Accordingly, ITK pixel coordinate (3 25 40) would be the same as Snap coordinate (4 26 41).