Syllabus:

 RADI  6880  Medical  Imaging  (v11):    Learn  Major  components  important  for  
computational  medical  imaging.    (Image  Reconstruction  and  Processing)  

 
Prerequisites?     Vector  Calculus  (required)  &    Linear  Álgebra  (or  equivalent).    Materials  in  this  class  are  
highly  geometrical.  It  is  essential  that  Students  have  solid  and  fluent  fundamental  
mathematics  and/or  computer  programming  experience  to  be  successful  in  this  course.        
 
Where  and  When?  Class  will  be  held  Wednesday,  Thursday  3:30-­‐4:45  pm  Room  113A  with  the  first  day  beginning  the  
th
week  starting  January  18 .  
 
References  for  the  Class?  
Main  Book-­‐  We    recommend  that  you  purchase  this  book  
Digital  Image  Processing  (3rd  Edition)  
Rafael  C.  Gonzalez  (Author),  Richard  E.  Woods  (Author)  
ISBN-­‐10:  013168728X  

 
Readings  for  the  Course,  we  will  provide  or  you  can  obtain  these  electronically  
 
Provided  on  the  Web  
 
Principles  of  Computerized  Tomographic  Imaging  
A.  C.  Kak  and  Malcolm  Slaney  
http://www.slaney.org/pct/pct-­‐toc.html  
 
Kalman  Filter  Tutorial:  Irfan  Essa  
http://www.cc.gatech.edu/classes/cs7322_98_spring/PS/kf1.pdf  
http://www.cc.gatech.edu/classes/cs7322_98_spring/PS/kf2.pdf  
Learning  with  Maximum  Likelihood  by  Andrew  W.  Moore  
http://www.autonlab.org/tutorials/mle13.pdf  
 
What  is  the  expectation  maximization  algorithm?  by  Chuong  B  Do    &  Serafim  Batzoglo  
   Nature  Biotechnology  26,  897  -­‐  899  (2008)  
http://www.nature.com/nbt/journal/v26/n8/full/nbt1406.html  
 
Bayesian  Readings  http://www.cs.cmu.edu/afs/cs.cmu.edu/Web/People/awm/tutorials/list.html  (includes  hyperlinks  below)  
Probability for Data Miners  
A Short Intro to Naive Bayesian Classifiers, Short Overview of Bayes Nets,
Bayesian Networks,,Inference in Bayesian Networks Learning Bayesian Networks,

 
We  provide  copies  from  this  book  (  reserve    or  paper  form).  
 
Image  Reconstruction  in  Radiology      
J.  Anthony  Parker  (Author)  
ISBN-­‐10:  0849301505  
 
Foundations  of  Medical  Imaging      
Z.  H.  Cho  (Author),  Joie  P.  Jones  (Author),  Manbir  Singh  (Author)  
ISBN-­‐10:  0471545732  

1
  
II.  Syllabus  
 

Note  the  starred  sections  below  (*)  contain  review  material.  Students  should  have  had  this  material  in  undergrad,  but  
after  we  go  over  these  sections,  students  will  be  completely  responsible  for  efficiently  this  sort  of  mathematics  (it’s  
needed  to  understand  the  latter  material  fluently.)    For  this  course  we  expect  you  to  be  fluent  in  these  methods  (hence  
the  review).    Mechanically  from  a  Mathematics  point  of  view,  students  should  be  solid.  Read  and/or  Glance  through  all  
reading  before  coming  to  each  class  (required).  
 
Part  0:  Pre-­‐Mathematical  Preliminaries  for  Image  Recon/Processing–      fast  review  of  mechanical  details,  work  on  lots  
of  problems  in  and  out  of  class  (has  1  review  homework  and  1  FT  hwk  and  a  Quiz)  
  Topic   Reading  (Make  sure  you  at  least   Lecturer  
preview  &  read  materials  before  class)  
1*   Transforms  (FT  Properties)  Homework  1  will    Gonzalez  Chapter  4  199-­‐257     Wu  
be  assigned  (graded).          Cho:  P  21-­‐38  and  Class  Notes    
2*   Fast  Review  II  (FT  properties),      Gonzalez  Chapter  4  199-­‐257   Wu  
Cho:  P  21-­‐38  and  Class  Notes  
3*   Review  (vectors,  linearity,  determinant,   Work  problems  in  class  based  on  first   Wu  
gradient,  independence,  dot  product,  curl,   homework  1  assigned  on  first  day.)    
Jacobian,  integration  by  parts,  chain  rule)   Homework  due  at  beginning  of  class  

4*   Transforms  (FT  Properties)  /  Sampling  Basic   Gonzalez  Chapter  4  199-­‐257   Wu  

Least  Squares/Normal  Equations      weighted   Cho:  P  21-­‐38,  Class  Notes  and  
least  squares.  Eigenvectors.   Parker  Chapter  24  (start)  
th
Deadline  A   Project  deadline  due  prior  to  5  class  (select  2-­‐4  possible  topics)–    nonbound  to  these  topics-­‐  graded    
Part  1:      Image  Manipulation  and  Radon  Transform  and  Circular  Reconstruction  (part  1  has  1  quiz  and  1  homework  
total  –  includes  sampling)  –    More  conventional  lecturing  for  here  on  out.  

5*   Interpolation  and  Entropy,  probability  I  and   Cho:  P39-­‐68;  Gonzalez  8.1.4  ,  glance   Wu  
Bayesian  I.  (some  new  material)   over  Parker  Ch.  10  &  Andrew  Moore  
6   Circular  Transforms  and  Properties     Gonzalez  Chapter  5.11,   Wu  
Kak  &  Slaney  Ch  3  
7   Filtered  Back  Projection   Gonzalez  Chapter  5.11,     Wu  
Kak  &  Slaney  Ch  3  
8   Filtered  Back  Projection   Gonzalez  Chapter  5.11,     Wu  
(continued)/ConeBeam   Kak  &  Slaney  Ch  3  
Part  2  Probabilistic  Methods  (part  2  has  1  quiz  (after  the  test)  and  1  homework  total)  
9*   Basic  Probability  and  Bayesian  Part  II   Parker  Chapter  10,  (continued)  and   Wu  
Parker  Ch  24(cont)  &  Andrew  Moore  
10   Stochastic  Processing    -­‐  Wiener  Filter   Ch  25(start),    and  mainly  Ch  26     Sonnad  
th
Deadline  B   Project  deadline  due  prior  to  11  topic  class,    select  1  topic,  start  milestones,  outline  -­‐graded  

11   Extensions  of  Wiener,  Bayesian  part  III.    Gonzalez  5.5-­‐5.10,      Chapter  25  ,    26  &   Wu  
Andrew  Moore  
12   Stochastic  Processing  -­‐  Kalman  Filtering   Kalman  reading  (Tom  Lacey  kf1.pdf)   Sonnad  
13   Overview/Review  of  Probabilistic  methods   Gonzalez  5.5-­‐5.10  Kalman  reading   Wu  
(from  lectures  10-­‐12).  Bayesian  part  IV.   Parker  Chapter  10  ,11,12,24,26      
 14   Midterm  TEST    I  includes  through  lecture  13  (test  is  at  night).  

2
  15   Stochastic  Processing/EM  (basic)  of  images      Do  &  Batzogolou  Basic  Primer,  Andrew   Sonnad  
Moore  (has  math  =more  important)  
***   PRE-­‐Proposal  Project  Presentation.   Commitment  to  project  –  Arrange    
(individual  meetings  with  Dr.  Wu)   Meeting  TIME  (not  graded)  
16   Stochastic  Processing  OSEM    or  Bayesian  V   Tentative,  dependent  on  skills  to  date   Wu  
Deadline  C   Project  outline  should  now  be  around  2-­‐3  pages  with  literature  search  and  milestones  ,  meet  with  Dr  
Wu  -­‐10-­‐15  min  -­‐graded  
Part  3:  Advanced/Modern  Reconstruction  Methods      (part  3  has  a  quiz)  
17   Tikhonov  regularization   Readings  provided  later   Ding  
18   Compressed  Sensing  I   Readings  provided  later   Cheng  
19   Compressed  Sensing  II  and  review   Readings  provided  later   Wu  
Deadline  D   Rough  draft  at  least  several  sections  of  your  project  (should  be  2-­‐5  page  draft  minimum),  highlight  
remaining  challenges  

Part  4:    Image  and  Signal  Processing  Methods  and  Edge  Detection  (has  1  homework,  and  maybe  1  quiz)  
20   Image  registration/Coordinate  Transform   Notes  from  AIR  do  Homework.   Wu  
21   Image  Enhancement  (smoothing/sharpening,   Gonzalez  Ch  10     Wu  
Detection)  
22   Edge  Detection  with  Canny  Filtering   Notes  and  Gonzalez  Ch  10     Wu  
23   Image  Segmentation   Gonzalez  Ch  10     Wu  
Deadline  E   Rough  draft  at  least  several  sections  of  your  project  (should  be  5-­‐10  page  draft  minimum),  highlight  
remaining  challenges.  Support  all  reference  documents  electronically.  -­‐graded  
  Part  5:    Advanced  and  Applied  Concepts  for  Image  Reconstruction  (maybe  1  quiz  after  test)  
24   Data  Fusion   Provided  by  P.  Vedula   Vedula  
25   “phase  reconstruction”,  wavelet  and  or  more   Pending  Progress.   Wu  
on    iterative  CT  with  ML-­‐EM”  (    if  time)  
26   Midterm  Test  II  (test  includes  primarily  sections  14  through  24  will  be  at  night).  
27   Image  Segmentation  with  Motion     Therapy  Paper  (tentative  if  time)   Wu  
28    Image  Perception  (  if  Parkhurst  is  available.)   Provided  by  Dr.    Parkhurst  or  Dee  Wu   Parkhurst