Methods In Medical Image Analysis - Spring 2015

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

John Galeotti
Usually meets with students after class
Teaching Assistant

Srivignesh Rajendran


Tuesday, 3:15 - 4:15 pm, NSH 4113
And by appointment

Syllabus (general)

Syllabus (ECE detailed format)

Meeting in GHC 4102
(at Carnegie Mellon University)

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

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:  6 radiology sessions and 0-2 (TBD) pathology sessions, 8:30-9:30 AM weekday mornings (and possibly other times optional for shadowing pathology).

Online schedule (same password), directions, and required UPMC confidentiality agreement. Reports should be emailed to your TA 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Last Year's Website has been archived.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

Assignment #4 - Registration (optional)

Final Project

Schedule--Subject to Change
(Future plans are tentative, based on the old 2014 schedule)

Note about videos: Lecture videos were recorded in 2012, and you can downlaod the lecture videos from the 2012 schedule here. 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 2014? Material Video and .pptx files
Week 1
Tu 1/13

Lecture 1: Introductions, purpose, Syllabus
Assignment #1 given

Power Point
Video (from 2012)
Th 1/15

Lecture 2: Math & probability background
Begin class with a short QUIZ on Snyder ch. 1-2
Pitt's add/drop-with-refund period ends on 16th (tomorrow)

Power Point
Video (from 2012)
Week 2
Tu 1/20

Lecture 3: Programming background:  C++ & Python

Power Point
Video (from 2012)
Th 1/22

Lecture 4: ITK background & basic usage
CMU's add/drop-with-refund period ends on 23rd (tomorrow)

Power Point
Video (from 2012)
Week 3
Tu 1/27
Y Lecture 5: Image characterization
Quiz #2 on Snyder ch. 4 (skip hexagonal coordinates on pp 57-59 & 71-73)

Power Point
Video (from 2012)

Th 1/29
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 2/5.

Power Point
Video (from 2012)
Week 4
Tu 2/3

Assignment #2 given on Monday - due 10pm on 2/12
Lecture 7
: Image relaxation: restoration & feature extraction
Quiz #5 on Snyder ch. 6
Later today: TA Help Session for Take-home quiz, 3:15 - 4:15 pm, NSH 4113

Power Point
Video (from 2012)
Th 2/5

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

Power Point
Video (from 2012)
Week 5
Tu 2/10

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)

Power Point
Video (from 2012)
Th 2/12

Lecture 10: Segmentation, part 1 continued (using lecture 9 notes, start with slide 8)
Discuss Shadow Program & signup procedure in class.

Notes for Today:

Assignment 2 is due at 10:00 pm today

Week 6
Tu 2/17

Lecture 11: Segmentation, part 3 (active contours)

Shadow Program — be sure to sign up for the Shadow Program THIS WEEK, beginning at 10:00 pm today (all previous signups will be removed).

Power Point
Video (from 2012)

Th 2/19
Y Class Cancelled:  Extreme cold + windchill, which are especially problemeatic for students having to travel back and forth between universities, and I might not be able to drive in.

Shadow Program signup ends tonight!
Shadow Program starts Monday--show up at 8 am until you know where you're going
Week 7
Tu 2/24

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

Also, Imaging Modalities if time allows.

How is the shadow program going?

Power Point
Video (from 2012)

Imaging Modalities Power Point (contains embedded movies)
Video (from 2012, skip to end for imaging modalities)

Th 2/26

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

Power Point
Video (from 2012)
Week 8
Tu 3/3
Y Lecture 14 Registration in depth (Insight into Images ch 10 + Viola & Wells)
Discuss Shadow Program Details, esp. Musculoskeletal
SVN accounts distributed sometime today
Power Point
Video (from 2012)
Th 3/5
Y Lecture 15 Deformable registration (Insight into Images ch 11)

Discuss final projects
Be sure to email me your tentative project proposals by the night of Thurday the 19th.

Assignment #3 given: Segmentation and pre-processing , due 10pm Tuesday the 17th.

Pitt's deadline to submit Monitored Withdrawal forms is 6th (tomorrow)

Power Point
Video (from 2012)

Power Point 2

Spring Break
3/10 - 3/12
  No Lectures  
Week 9
Tu 3/17
Y Lecture 16: ITK images & iterators
Power Point
Video (from 2012)
Th 3/19
Y Lecture 17: ITK pipeline, including reading/writing images and connecting to SimpleITK
Tentative project proposals due tonight
Power Point
Video (from 2012)
Week 10
Tu 3/24
Y Lecture 18 Mathematical morphology & image matching
Quiz on Snyder 7.1-7.5 & 13.1-13.5

Power Point
Video (from 2012)
Th 3/26
Y Lecture 19: ITK filters: how to write them (neighborhoods, image boundaries, & numeric traits)

Power Point
Video (from 2012)

  Note: CMU's drop-without-withdrawl period ends on March 30th (Monday)  
Week 11
Tu 3/31
Y Lecture 20: ITK filters, part 2 (advanced filter creation & misc. tools)
CMU's drop-without-withdrawl period ends on March 31st (yesterday!)
Power Point
Video (from 2012)
Th 4/2

Lecture 21a: ITK Paths

Lecture 21b: Summarize Cootes and Taylor ASM (Cootes CVIU 1995)

Power Point
Video (from 2012)

Power Point (public version)

Week 12
Tu 4/7


Lecture 22: Open source software development philosophy, and Visualization Power Point
Th 4/9
Y Guest Lecture: MRI/DTI (see also brain anatomy and the fiber track image gallery)  
Week 13
Tu 4/14

NeuroPathology -- Normal class time, meet at UPMC:

Please try to arrive before 10:30am

  1. Enter Scaife Hall from the main doors on Terrace street (directly across from the Peterson event center).
  2. Immediately inside are a bank of elevators: Take one up to the 7th floor.
  3. Go right as you exit the elevator and go through a set of double doors.
  4. Ron Hamilton's office and the microscope room are right there

Th 4/16
  No Lecture - CMU Spring Carnival  
Week 14
Tu 4/21
  Student project presentations (see random order email)
(Each presentation must be between 4.5 - 5.5 minutes long.)
Everyone's power-point slides due by 10 AM today!
Th 4/23
  Student project presentations & Projects Due  
  Fri 4/24   Optional registration homework given, due 10am Saturday morning  
Remaining Lecture Fragments:
Potential Lectures:
      Itk Video (w/ OpenCV?)  
      Lecture 24: Advanced Shape Analysis, Shape Comparisons, and Segmentation Validation (includes spherical harmonics, medial, DICE, etc.)  
      NeuroPathology at 10:30 today! Meet at UPMC, not at CMU. Follow emailed directions.