Methods In Medical Image Analysis - Spring 2009

BioE 2630 (Pitt) : 16-725 (CMU RI) : 42-735 (CMU BME)

Instructor: John Galeotti
(galeotti+miia ATcs.cmu.edu)

Teaching Assistant: Doug Nelson
(dan13+miia ATpitt.edu)

Syllabus

Meeting in CFA 213
(at Carnegie Mellon University)

Class begins Tuesday, Jan. 13th!
Class ends Thursday, April 23rd.


Lecture and Shadow Program / Times and Locations

We comply with both the U. Pitt. and CMU calendars. Lectures are Tuesday and Thursday from 10:30-11:45 AM, in CFA 213, Carnegie Mellon University.

Shadow Program - 5 sessions 8:30-9:30 AM, weekday mornings, see online schedule (same password) and directions.

Last Year's Website has been archived.


Textbooks, Downloads, & Other References

myITKgui - Warning: Does not work on Mac (specifically on my intel Mac with VTK5.x)


Assignment #1 - Introductory Email

Assignment #2 - Install and Test: ITK, VTK, & FLTK

Assignment #3 - Fun with Filters

Assignment #4 - Segmentation Competition


Schedule--Subject to Change

Week 1
Tu 1/13
Lecture 1: Introductions, purpose, Syllabus, & imaging modalities
Assignment #1 given.
 
Th 1/15
Lecture 2: Programming background  
   
Week 2
Tu 1/20

Lecture 3: ITK background & basic usage
Assignment #2 given. Due by midnight on 1/28.

 
Th 1/22
Lecture 4: Math & probability background
Begin class with a short QUIZ on Snyder ch. 1-2
Recommend also looking at 16-720's Math Tutorial
 
   
Week 3
Tu 1/27
Lecture 5: ITK images & iterators
 
Th 1/29
Lecture 6: Image characterization
Quiz on Snyder ch. 4-5.3 (skip hexagonal coordinates on pp 57-59 & 71-73)
 
   
Week 4
Tu 2/3
No Lecture: I have a new baby boy!
 
Th 2/5
Lecture 7: Linear processing 1 & ITK pipeline
Be sure to sign up for the Shadow Program THIS WEEK.
Assignment #3 given (do not attempt Part 3 until after Lecture 9).
 
   
Week 5
Tu 2/10
Lecture 8: Linear processing 2
Quiz on Snyder 5.4-5.6,5.8-5A (through page 101, but skip 5.7)
 
Th 2/12
Lecture 9: ITK filters: how to write them (neighborhoods & numeric traits)
 
   
Week 6
Tu 2/17
Lecture 10: Image relaxation: restoration & feature extraction
Quiz on Snyder ch. 6
 
Th 2/19
Lecture 11: ITK filters (advanced filter creation & misc. tools)  
   
Week 7
Tu 2/24

Lecture 12: Segmentation, part 1
Quiz on Snyder ch. 8 (skip 8.3.2 on pp. 189-196 & 8A.1.1 on pp. 208-209)

 
Th 2/26

Lecture 13: Segmentation, part 2 (continues using lecture 12 notes)
Also, be sure to email me your project proposals by Friday night (the 27th)!

 
   
Week 8
Tu 3/3

Lecture 14: Segmentation, part 3 (active contours)
May also start lecture 15, below!

 
Th 3/5
Lecture 15: ITK registration  
   
Spring Break
3/10 - 3/12
No Lectures
But get started on your projects
 
       
Week 9
Tu 3/17
Lecture 16: Mathematical morphology & image matching
Quiz on Snyder 7.1-7.5 & 13.1-13.5
 
Th 3/19
Lecture 17: Level set segmentations & parametric transforms (Snyder 8.5.2 + Insight into Images ch 8 & Snyder 11.1-11.6)
Quiz on Snyder 11.1-11.6
 
   
Week 10
Tu 3/24

Lecture 18: Cootes and Taylor ASM (Cootes CVIU 1995) (based on 2008 guest lecture by Ken Urish)

 
Th 3/26

Lecture 19: Shape, then finish ASM.
Quiz on Snyder ch. 9 (read 9.1-9.8, 9.12-9.14)

 
   
Week 11
Tu 3/31
Lecture 20: Registration in depth (Jen Mercer's slides: Insight into Images ch 10 + Viola & Wells)  
Th 4/2
Lecture 21: Deformable registration
Assignment #4 given.
 
   
Week 12
Tu 4/7
Lecture 22: Scientfic paper review: ITK Paths  
Th 4/9
Lecture 23: Guest lecture on DTI (see also brain anatomy and the fiber track image gallery)  
   
Week 13
Tu 4/14
Lecture 24: ITK and open source software development philosophy, and Visualization  
Th 4/16
No Lecture - CMU Spring Carnival  
   
Week 14
Tu 4/21
Student project presentations  
Th 4/23
Student project presentations & Projects Due