Methods In Medical Image Analysis - Spring 2012

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

John Galeotti
Teaching Assistants

Vikas R.S.


“Jackie” Chen


Syllabus (general)

Syllabus (ECE format)

Meeting in GHC 5222
(at Carnegie Mellon University)

Class begins Tuesday, Jan. 17th!
Class ends Thursday, May 3rd.

Lecture 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 5222, Carnegie Mellon University.

Shadow Program Times, Locations, & Details

Shadow Program:  5-8 sessions, 8:30-9:30 AM weekday mornings (and possibly other times optional for shadowing pathology).

Online schedule (same password) and directions. Reports should be emailed to Jackie and Galeotti.

Textbooks, Downloads, & Other References

Last Year's Website has been archived.


Assignment #1 - Introductory Email

Assignment #2 - Get ITK & SimpleITK installed, etc.

Assignment #3 - Use SimpleITK to do Segmentation and Pre-processing


Final Project

Schedule--Subject to Change

Note about videos: Be sure to download the videos (right-click the video's link then select either "download" or "save-as") rather than try to watch them in your browser. Please let me know if you notice any problems or video content that should be either fixed or trimmed out if it's not relevant to a general audiance (please reference the 2012 lecture number and the playing time into the video at which the problem occurs).

Week # Date Updated for 2012? Material Video and .pptx files
Week 1
Tu 1/17

Lecture 1: Introductions, purpose, Syllabus
Assignment #1 given
Pitt's add/drop period ends today

Power Point
Th 1/19
Y Lecture 2: Programming background:  C++ & Python Power Point
Week 2
Tu 1/24

Lecture 3: Math & probability background
Begin class with a short QUIZ on Snyder ch. 1-2

Power Point
Th 1/26
Y Lecture 4: ITK background & basic usage (& imaging modalities?)
Assignment #2 given
CMU's add/drop-with-refund period ends on 27th (tomorrow)
Power Point
Week 3
Tu 1/31

Lecture 5: Image characterization
Quiz #2 on Snyder ch. 4 (skip hexagonal coordinates on pp 57-59 & 71-73)

Power Point
Th 2/2
Y Lecture 6: Linear processing
Quiz #3 on Snyder 5.1-5.6,5.8-5A (through page 101, but skip 5.7)
Take-home quiz #4 assigned - due in class on 2/9.
Power Point
Week 4
Tu 2/7

Lecture 7: Image relaxation: restoration & feature extraction
Quiz #5 on Snyder ch. 6
Later today: TA Help Session for Take-home quiz, 4:30-5:30 PM at GHC 4301

Power Point
Th 2/9

Lecture 8: ITK registration
Take-home quiz #4 due in class.

Power Point
Week 5
Tu 2/14

Lecture 9: Segmentation, part 1
Quiz #6 on Snyder ch. 8 (skip 8.3.2 on pp. 189-196 & 8A.1.1 on pp. 208-209)
Discuss Shadow Program & signup procedure in class.
Shadow Program -- be sure to sign up for the Shadow Program THIS WEEK, beginning at 6 PM on the 15th.

Power Point
Th 2/16
Y Lecture 10: Segmentation, part 2 (continue using lecture 9 notes, start with segmentation by thresholding) Video
Week 6
Tu 2/21

Lecture 11: Segmentation, part 3 (active contours)
Discuss Shadow Program (which starts the 22nd, i.e. tomorrow)

Power Point
Th 2/23
Y Lecture 12: Level set segmentations & (briefly begin) parametric transforms (Snyder 8.5.2 & Snyder 11.1-11.6) [not required, but recommended: Insight into Images ch 8]
Quiz on Snyder 11.1-11.6
Power Point
Week 7
Tu 2/28

Lecture 13: Shape (& finish parametric transforms)
Quiz on Snyder ch. 9 (read 9.1-9.8, 9.12-9.14)

Power Point
Th 3/1

Lecture 14: Mathematical morphology & (briefly begin) image matching
Quiz on Snyder 7.1-7.5 & 13.1-13.5
Discuss final projects
Be sure to email me your tentative project proposals by the Wed night of the 14th (or sooner, esp. for CMU students)!
Pitt's deadline for students to submit Monitored Withdrawal forms to dean's office is the 2nd (tomorrow)

Power Point 1
Power Point 2
Pitt Spring Break
3/6 - 3/8

No Lectures

CMU Spring Break
3/13 - 3/15
  No Lectures  
Week 8
Tu 3/20
Y Lecture 15: ITK images & iterators
Assignment #3 given: Segmentation and pre-processing

Power Point

Th 3/22

Lecture 16: ITK pipeline, including connecting to SimpleITK (and possibly Imaging Modalities also)

Power Point
Week 9
Tu 3/27
Y Lecture 17: ITK filters: how to write them (neighborhoods & numeric traits) Power Point
Th 3/29
Y Lecture 18: ITK filters, part 2 (advanced filter creation & misc. tools)
CMU's drop-without-withdrawl period ends on 30th (tomorrow)
Power Point
Week 10
Tu 4/3
Y Lecture 19: Registration in depth (Insight into Images ch 10 + Viola & Wells)
Power Point
Th 4/5
Y Lecture 20: Deformable registration & Imaging Modalities

Power Point 1
Power Point 2

Week 11
Tu 4/10
Y Lecture 21: ITK Paths Power Point
Th 4/12
Y Lecture 22: ITK and open source software development philosophy, and Visualization Power Point
Week 12
Tu 4/17

Project working session--bring your laptops--attendance optional.

Th 4/19
  No Lecture - CMU Spring Carnival  
Week 13
Tu 4/24
  Student project presentations (schedule)
(Each presentation must be between 4.5 - 5.5 minutes long.)
Everyone's power-point slides due by 10 AM today!
Th 4/26
  Student project presentations & Projects Due  
Week 14
Tu 5/1
  Pitt not in session  
Th 5/3
  Pitt not in session  
Remaining Lecture Fragments:
Lecture 7 GNC onward (when did I tack this on?), Lecture 14 Image Matching  
Potential Lectures:
      Guest Lecture: MRI/DTI (see also brain anatomy and the fiber track image gallery)  
      Itk Video (w/ OpenCV?)  
      Cootes and Taylor ASM (assuming part of ITKv4) (Cootes CVIU 1995) (based on 2008 guest lecture by Ken Urish)  

Meet at UPMC, not at CMU

Directions have been emailed; Email your instructor now if you did not get them.