Methods In Medical Image Analysis - Spring 2010

BioE 2630 (Pitt) : 16-725 (CMU RI) : 18-791 (CMU ECE) : 42-735 (CMU BME)

Instructor
John Galeotti
galeotti+miia ATcs.cmu.edu
 
Teaching Assistants
Doug Nelson
(Quizzes)
dan13+miia ATpitt.edu

Benjamin Schmidt
(Shadow Program)
schmidt.pittTA ATgmail.com

Syllabus

Meeting in GHC 4101
(at Carnegie Mellon University)

Class begins Tuesday, Jan. 12th!
Class ends Thursday, April 29th.

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 GHC 4101, Carnegie Mellon University.

Shadow Program - 5 sessions 8:30-9:30 AM, weekday mornings, see online schedule (same password) and directions. Reports should be emailed to Schmidt and Galeotti.

Last Year's Website has been archived.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)

Assignments--Subject to Change until officially assigned
(Until an assignment is actually assigned, it is most lilely a copy of last year's assignment. I leave the old copies here in advance to give you an idea of how much work you will have to do in the future. Acordingly, please do not start an assignment until it is actually assigned.)

Assignment #1 - Introductory Email

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

Assignment #3 - Fun with Filters

Assignment #4 - Segmentation Competition

Assignment #5 - Registration

Schedule--Subject to Change (initially filled in with last year's schedule)

Week 1
Tu 1/12
 Lecture 1: Introductions, purpose, Syllabus, & imaging modalities
Th 1/14
 Lecture 2: Programming background
Assignment #1 given
 
Week 2
Tu 1/19

Lecture 3: ITK background & basic usage (& imaging modalities from Lecture 1)
Assignment #2 given
Th 1/21
 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 1/26

Lecture 5: ITK images & iterators (& optimization/HMM from Lecture 4)
Th 1/28
 Lecture 6: Image characterization
Quiz #2 on Snyder ch. 4-5.3 (skip hexagonal coordinates on pp 57-59 & 71-73)
 
Week 4
Tu 2/2

Lecture 7: Finish pixel access from Lecture 5, Shadow Program, & ITK pipeline
Be sure to sign up for the Shadow Program THIS WEEK
Th 2/4

Lecture 8: Finish ITK Pipeline, begin Linear processing
Quiz #3 on Snyder 5.4-5.6,5.8-5A (through page 101, but skip 5.7)
Assignment #3 given (do not attempt Part 3 until after Lecture 9).
 
Week 5
Tu 2/9
 No Lecture
Both universities cancelled classes due to the snow
Th 2/11
 Lecture 9: ITK filters: how to write them (neighborhoods & numeric traits)
Also: Continue discussing linear processing
Take-home quiz #4 assigned (if we get to the lecture material)
 
Week 6
Tu 2/16
 Lecture 11: Image relaxation: restoration & feature extraction
Quiz on Snyder ch. 6
Th 2/18
 Lecture 12: ITK filters (advanced filter creation & misc. tools)
 
Week 7
Tu 2/23

Lecture 13: Segmentation, part 1
Quiz on Snyder ch. 8 (skip 8.3.2 on pp. 189-196 & 8A.1.1 on pp. 208-209)

Th 2/25

Lecture 14: 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 3/2

Lecture 15: Segmentation, part 3 (active contours)
May also start lecture 15, below!
Th 3/4
 Lecture 16: ITK registration
 
Spring Break
3/9 - 3/11
 No Lectures
But get started on your projects
     
Week 9
Tu 3/16
 Lecture 17: Mathematical morphology & image matching
Quiz on Snyder 7.1-7.5 & 13.1-13.5
Th 3/18
 Lecture 18: 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 3/23

Lecture 19: Cootes and Taylor ASM (Cootes CVIU 1995) (based on 2008 guest lecture by Ken Urish)
Th 3/25

Lecture 20: Shape, then finish ASM.
Quiz on Snyder ch. 9 (read 9.1-9.8, 9.12-9.14)

 
Week 11
Tu 3/30
 Lecture 21: Registration in depth (Jen Mercer's slides: Insight into Images ch 10 + Viola & Wells)
Th 4/1
 Lecture 22: Deformable registration
Assignment #4 given.
 
Week 12
Tu 4/6
 Lecture 23: Scientfic paper review: ITK Paths
Th 4/8
 Lecture 24: Guest lecture on DTI (see also brain anatomy and the fiber track image gallery)
 
Week 13
Tu 4/13
 Lecture 25: ITK and open source software development philosophy, and Visualization
Th 4/15
 No Lecture - CMU Spring Carnival
 
Week 14
Tu 4/20
 Student project presentations
Th 4/22
 Student project presentations
     
Week 15
Tu 4/27
 Student project presentations
Th 4/29
 Student project presentations & Projects Due