Back to E
Morris homepage |
Back to class homepage |
|||||||||||||||||||||||||||||||
Lecture # | Date | day | special
dates, possible conflicts |
Reading (in books) | Reading (of journal articles) | Other reading (watch this spcae) | Homework | |||||||||||||||||||||||||
Actual
lecture |
Originally planned Lecture topic | textbook - chapter (due by class on this date) | click here for
all articles |
|||||||||||||||||||||||||||||
8/23/2006 | wed | organization |
organizational
meeting; address proposal to move class
location to R2 Bldg conference room E-124 and move class time to 4pm? |
1. excerpt
from Holtzmann-Kevles 2. excerpt from Levi |
Homework 1 |
|||||||||||||||||||||||||||
(see sources) |
||||||||||||||||||||||||||||||||
1 | 8/28/2006 | mon | canceled |
Introduction to tracer kinetics and input-output models | Lassen and Perl: 1; Godfrey chapter 1, | |||||||||||||||||||||||||||
2 | 8/30/2006 | wed | intro
to tracers - intravascular |
constant infusion; the Fick principle | Lassen and
Perl: 2 chaps 1& 2 in 1 file) |
|||||||||||||||||||||||||||
9/4/2006 | mon | Labor Day? | ||||||||||||||||||||||||||||||
3 | 9/6/2006 | wed | intro to
tracers-freely diffusible-1 |
L&P: 3 and L&P:4 | Homework 1 Answers | |||||||||||||||||||||||||||
intro to
tracers-freely diffusible-2 |
returned |
|||||||||||||||||||||||||||||||
4 | 9/11/2006 | mon | Kety
method lecture 1 |
L&P:5 and L&P:6 | |
Homework
2 |
||||||||||||||||||||||||||
5 | 9/13/2006 | wed | Kety
method lecture 2 |
Kety
and Schmidt 1945 - the Xenon method Kety and Schmidt 1948 J Ckin Invest |
Homework 3 |
|||||||||||||||||||||||||||
6 | 9/18/2006 | mon | The Krogh
cylinder Set up mass balances axially and radially... solve the model |
Fournier
chap 5 pg 203-215 |
Krogh
J Physiol 1919 |
Homework
3 answers - handed out |
||||||||||||||||||||||||||
7 | 9/20/2006 | wed | The
Renkin-Crone model Extraction Flow-limited case Diffusion-limited case |
Fournier chap 5 pg 203-215 | Crone, Acta Physiol Scan, 1963 |
Homework
4 assigned: examples 5.12 and 5.13 in Fournier |
||||||||||||||||||||||||||
8 | 9/25/2006 | mon |
Crone
measurement of capillary permeability. Indicator diffusion method. |
Capillary Permeability | L&P:11 (Multiple indicators, capilary permeability) |
|||||||||||||||||||||||||||
9 | 9/27/2006 | wed | Compartmental
Models Well-mixed compartments Is the Kety model either? |
Compartmental analysis |
L&P:
10 cmpt'mtl models |
NIBIB
news release MR tracks organ rejection |
Homework
3 returned |
|||||||||||||||||||||||||
10 | 10/2/2006 | mon | Yom Kippur | |||||||||||||||||||||||||||||
11 | 10/4/2006 | wed | linear, time-invariant , 1st order systems Compartmetntal models Transition Matrix |
Godfrey
chapter 2 |
Homework
4 returned |
|||||||||||||||||||||||||||
12 | 10/9/2006 | mon | transition
matrix., eigenvectors, 1 and 2 compartment models. Step and impulse
response |
examples of compt'ml models |
Godfrey chapter 2
|
Papenheimer
et al., 1951: |
For
HW #5 matlab example code (right click to download) numerical solution of) ODEs & symbolic math solution of ODEs |
|||||||||||||||||||||||||
13 | 10/11/2006 | wed | solving
examples of 1 and 2 compartmental models |
examples of compt'ml models | Godfrey
Chap 3 |
Please
read for class: Patlak 1983 |
||||||||||||||||||||||||||
14 | 10/16/2006 | mon | Derivation
of Patlak plot multiple time graphical method for systems with an irreversible trap. |
|||||||||||||||||||||||||||||
15 | 10/18/2006 | wed | Generalization of the Patlak plot; The Logan plot for reversible receptor tracers Biases in the Logan plot |
|
Patlak
1985 Logan 1990; Slifstein 2000; Logan 2003 (required) |
|||||||||||||||||||||||||||
16 | 10/23/2006 | mon | Input- output models CBV,CBF,MTT with MR | Ostergaard,
1996 Ostergaard, 2004 Axel chapter in LeBihan book . |
Meier and Zierler, 1954; Multiple Indicator Dilution method | |||||||||||||||||||||||||||
17 | 10/25/2006 | wed | DSC-MR perfusion | data
files Perfusion Imaging Tutorial |
A.Smith
2000, JMRI Warach et al Neuroradiology 06, Tofts Chap 11 |
Perfusion
Tutorial (see slides on SVD) must use IE to view |
new
MR contrast agent sensitive to calcium new MR contrast agent sensitive to gene expression |
HW #6 assignment data files |
||||||||||||||||||||||||
18 | 10/30/2006 | mon | Permeability
with DCE-MRI (T1-wtd) |
|
Tofts chap 10. | blood flow and other stuff with MR, Tofts et al JMRI 1999 | Choyke article in Diagnostic Imaging | |
||||||||||||||||||||||||
19 | 11/1/2006 | wed | Permeability
with MR - finish standard Tofts derivation. Add adiabatic approx to tissue homogeneity mode. |
|
St Lawrence & Lee Adiabatic approx to tissue homogeneity model |
Tofts
1997, JMRI Modeling Tracer kinetics; |
|
|||||||||||||||||||||||||
20 | 11/6/2006 | mon | Setting
up the Tissue-Homogeneity Model |
Johnson and Wilson, 1966 St Lawrence and Lee 1998. |
OTHER STUFF | OTHER STUFF |
||||||||||||||||||||||||||
21 | 11/8/2006 | wed | Implementing
deconvolution via Fourier Transpose or SVD ala Ostergaard |
Ostergaard, 1996 Press et al (Numerical Recipes) |
Spilker
2001 Silvey chapter 3,4 |
|||||||||||||||||||||||||||
22 |
11/13/2006 |
mon |
Solving
the Tissue Homog model via the "Adiabatic assumption" |
St
Lawrence & Lee Adiabatic approx to tissue homogeneity model |
GLLS;
Comparison of fitting methods Feng 1996; Muzic 2006 |
|||||||||||||||||||||||||||
23 | 11/15/2006 | wed | Demo of MR perfusion software Review of Homework. Applications of DCE-MR in cancer. Choice of flow model. |
MEDx Buckley et al Radiology, 2004 Harrer et al, 2004 |
identifiability Godfrey chapters 5-8 |
|||||||||||||||||||||||||||
24 | 11/20/2006 | mon | Permeability
with MR - Patlak analysis. F-statistic, Sensitivity analysis. |
Buckley
MRM 2002; Ewing et al Vascular permeability by MR |
||||||||||||||||||||||||||||
11/22/2006 | wed | NO CLASS - THANKSGIVING | ||||||||||||||||||||||||||||||
25 | 11/27/2006 | mon | Weighted
linear least squares regression |
Cobelli,
Chapter 8.1-8.5 |
Cunningham, 1991; Gunn, 1997 | reference region models | ||||||||||||||||||||||||||
26 | 11/29/2006 | wed | Weighted
nonlinear least squares regression, goodness of fitl, choice of model |
Cobelli Chap 8. |
Logan 1996; Ichise 1996; | reference region graphical methods and comparison | ||||||||||||||||||||||||||
PAPER PRESENTATIONS |
||||||||||||||||||||||||||||||||
27 |
12/4/2006 |
mon |
1. Ktrans by 1st pass model (Haroon et al 2004) |
Cunningham, 1993 | spectral analysis | |||||||||||||||||||||||||||
28 | 12/6/2006 | wed | 1.
Weighted integral method for blood flow (Alpert
et al 1984) 2. Perf and Perm mapping of gliomas (Koh et al, 2006) |
|
Gunn 2002 | |||||||||||||||||||||||||||
29 | 12/11/2006 | mon | 1 Bias in
Graphical Methods (Logan
2003) 2 BBB leakage with MR (Tofts and Kermode 1991) 3 Model for Flow and Perm (Bazelaire et al 2005) |
Turkheimer, 2002; Cselenyi 2006 | Wavelets; Comparison of methods | |||||||||||||||||||||||||||
30 | 12/13/2006 | wed | Final
Exam 4-5:30pm |
|||||||||||||||||||||||||||||
Other
Topics |
||||||||||||||||||||||||||||||||
Syllabus revised - Nov 12, 2006 - EDM) | ||||||||||||||||||||||||||||||||
TEXTS | ||||||||||||||||||||||||||||||||
AUTHORS | TITLE | PUBLISHER | Year | |||||||||||||||||||||||||||||
Lassen and Perl | Tracer Kinetic Models in Medical Physiology | Raven Press | 1979 | |||||||||||||||||||||||||||||
Cobelli, Foster, Toffolo | Tracer Kinetics in Biomedical Research | Kluwer Academic | 2000 | |||||||||||||||||||||||||||||
Silvey | Statistical Inference | Chapman & Hall/CRC | 2003 | |||||||||||||||||||||||||||||
Godfrey | Compartmental Models and their Application | Academic | 1983 | |||||||||||||||||||||||||||||
Jacquez | Compartmental Analysis in Biology and Medicine | U Michigan Press | 1985 | |||||||||||||||||||||||||||||
Holtzmann-Kevles | Naked to the Bone: Medical Imaging in the 20th Century | Addison Wesley | 1997 | |||||||||||||||||||||||||||||
Levi | George De Hevesy Life and Work | Rhodos |
1986 | |||||||||||||||||||||||||||||
supplementary texts | ||||||||||||||||||||||||||||||||
Carson, Cobelli, Finkelstein | The Mathematical Modeling of Metabolic and Endocrine Systems | Wiley | 1983 | |||||||||||||||||||||||||||||
Riggs | The Mathematical Approach to Physiological Problems | MIT Press | 1970 | |||||||||||||||||||||||||||||
Endrenyi (ed) | Kinetic data analysis. design and analysis of enzyme experiments | Springer | 1981 | |||||||||||||||||||||||||||||
Feinenedegen et al | Molecular Nuclear Medicine | Springer | 2003 | |||||||||||||||||||||||||||||
Fournier |
Basic Transport Phenomena in Biomedical Engineering |
Taylor and Francis |
2006 | |
||||||||||||||||||||||||||||
Valk
et al |
Positron Emission Tomography |
Springer |
||||||||||||||||||||||||||||||
LeBihan |
Diffusion and Perfusion
Magnnetic Resonance Imaging |
Raven Press |
1995
|
|||||||||||||||||||||||||||||
Buxton |
Intro to Functional Magnetic
Resonamce Imaging |
Cambridge |
2002 |
|||||||||||||||||||||||||||||
Phelps |
Positron Emission Tomography and
Autoradiography |
Raven |
1986 |
|||||||||||||||||||||||||||||
Dunn et al |
Numerical Methods in Biomedical
Engineering |
Academic |
2005 |
|||||||||||||||||||||||||||||
Press et al |
Numerical Recipes in C |
Cambridge |
1992 |
|||||||||||||||||||||||||||||
key to lecture schedule |
||||||||||||||||||||||||||||||||
no lecture - vacation day | ||||||||||||||||||||||||||||||||
possible conflict - may need to reschedule | ||||||||||||||||||||||||||||||||
definite conflict - lecture canceled | ||||||||||||||||||||||||||||||||
tentative times for class presentations and/or final exam |