Methods In Medical Image Analysis - Spring 2011

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
Samantha Horvath
(Quizzes)
shorvath+miia ATcs.cmu.edu

Vikas R.S.
(Shadow Program)

vir16+miia ATpitt.edu

Syllabus (general)

Syllabus (ECE format)

Classroom Change:

Meeting in GHC 4101
(at Carnegie Mellon University)
(* Was originally in GHC 4102)

Class begins Tuesday, Jan. 11th!
Class ends Thursday, April 28th.


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 4102, 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 your TA 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Last Year's Website has been archived.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

Assignment #3 - Fun with Filters

Assignment #4 - Registration

Assignment #5 - Segmentation Competition

Final Project


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

Week # Date Updated for 2011? Material
Week 1
Tu 1/11
Y Lecture 1: Introductions, purpose, Syllabus
Th 1/13
Y Lecture 2: Programming background
Assignment #1 given
   
Week 2
Tu 1/18
Y

Lecture 3: Math & probability background
Begin class with a short QUIZ on Snyder ch. 1-2
Recommend also looking at 16-720's Math Tutorial
Pitt's add/drop period ends today

Th 1/20
Y Lecture 4: ITK background & basic usage (& imaging modalities from Lecture 1)
Assignment #2 given
CMU's add/drop-with-refund period ends on 21st (tomorrow)
   
Week 3
Tu 1/25
Y

Lecture 5: ITK images & iterators

Th 1/27
Y Lecture 6: Image characterization
Quiz #2 on Snyder ch. 4-5.3 (skip hexagonal coordinates on pp 57-59 & 71-73)
   
Week 4
Tu 2/1
Y

Lecture 7: Linear processing
Quiz #3 on Snyder 5.4-5.6,5.8-5A (through page 101, but skip 5.7)
Take-home quiz #4 assigned - due in class on 2/10.

Th 2/3
Y

Guest Lecture: Lecture 8: ITK pipeline and probably begin ITK filters
Shadow Program -- be sure to sign up for the Shadow Program THIS WEEK

   
Week 5
Tu 2/8
Y Lecture 9: ITK filters: how to write them (neighborhoods & numeric traits), also resume Lecture 6 starting with ridges
Th 2/10
Y Lecture 10: ITK filters, part 2 (advanced filter creation & misc. tools)
Take-home quiz #4 due in class.
Assignment #3 given.
   
Week 6
Tu 2/15
Y

Lecture 11: Image relaxation: restoration & feature extraction
Quiz #5 on Snyder ch. 6
Discuss Shadow Program (which starts the 16th, i.e. tomorrow)

Th 2/17
Y Lecture 12: ITK registration
Discuss final projects
   
Week 7
Tu 2/22
Y

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)
Also, be sure to email me your project proposals by Friday night (the 26th)!

Th 2/24
Y

Lecture 14: Segmentation, part 2 (continue using lecture 13 notes), also resume Lecture 12 starting with Centered Transforms
Assignment #4 on registration given

   
Week 8
Tu 3/1
Y

Lecture 15: Segmentation, part 3 (active contours)

Th 3/3
Y Lecture 16: Registration in depth (Jen Mercer's slides: Insight into Images ch 10 + Viola & Wells)
   
Spring Break
3/8 - 3/10
  No Lectures
But get started on your projects (you still have hw5 coming as well!)
       
Week 9
Tu 3/15
Y 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
Assignment #5 on segmentation given.
Th 3/17
Y Lecture 18: Mathematical morphology & image matching
Quiz on Snyder 7.1-7.5 & 13.1-13.5
   
Week 10
Tu 3/22
Y Lecture 19: Cootes and Taylor ASM (Cootes CVIU 1995) (based on 2008 guest lecture by Ken Urish)
Th 3/24
Y Lecture 20: Shape
Quiz on Snyder ch. 9 (read 9.1-9.8, 9.12-9.14)
CMU's drop-without-withdrawl period ends on 28th (Monday)
   
Week 11
Tu 3/29
  Lecture 19: Deformable registration
Th 3/31
 

Lecture 23: Scientfic paper review: ITK Paths
Sign up for your presentation date: online signup begins at 9 PM tonight (and ends on Monday).

   
Week 12
Tu 4/5
  ? Pathology ?
Th 4/7
  ? Pathology ?
   
Week 13
Tu 4/12
  Lecture 24: ITK and open source software development philosophy, and Visualization
Th 4/14
  No Lecture - CMU Spring Carnival
   
Week 14
Tu 4/19
  Student project presentations
Th 4/21
  Student project presentations
       
Week 15
Tu 4/26
  Student project presentations
Th 4/28
  Student project presentations & Projects Due
       
Potential Lectures:    
      Lecture 25: Guest lecture on DTI (see also brain anatomy and the fiber track image gallery)