Medical Imaging

Fundamentals of Medical Imaging

Spring 2012

Tuesday, Thursday 12:30 PM to 1:50 PM , 109 NH

4328_5339Sp12TH_EXAM_I

Medical_Imaging_Spring12TH_Final

Instructor: Kambiz Alavi, PhD, Professor, Electrical Engineering

alavi@uta.edu, 540 Nedderman Hall, 817/272-5633, fax 817/272-2253

GTA: Shaoshu Sha shaoshu.sha@gmail.com

Office Hours: 3:30 - 6:30pm Tues, and 10am - 1:00pm on Wedn, in IEEE mentor office, NH 132.

WEEK 1:

Introduction:

http://www.eecs.umich.edu/~dnoll/BME516/intro.pdf

http://www.eecs.umich.edu/~fessler/course/516/l/noll,516,intro-jf.ppt

http://fmri.ucsd.edu/ttliu/be280a_10/BE280A10_intro.pdf

http://rst.gsfc.nasa.gov/Intro/Part2_26d.html

http://www.colorado.edu/physics/2000/tomography/projections.html

http://trshare.triumf.ca/~fretiere/TSI07/Talk/LecomteDay2.pdf

http://trshare.triumf.ca/~fretiere/TSI07/Talk/LecomteDay1b.pdf

http://trshare.triumf.ca/~fretiere/TSI07/Talk/LecomteDay1a.pdf

http://engineering.dartmouth.edu/courses/engs167/19%20Nuclear%20Medicine.pdf

http://engineering.dartmouth.edu/courses/engs167/20%20PET%20Imaging.pdf

MATLAB Tutorial http://www.engin.umich.edu/group/ctm/home.text.html

http://www.mathworks.com/academia/student_version/

Image Processing http://en.wikipedia.org/wiki/Histogram_equalization

https://www-ee.uta.edu/Online/Alavi/ee5359_bme5300/2006spring/medical_image_processing_1.pdf

ee4328-5339Spring12/histogram_equalization.pdf

WEEK 2:

Revised ee4328-5339Spring12/Lec_Jan_24_2012KA1.ppt Revised

ee4328-5339Spring12/2dCylindricalFourier.PDF

Linear systems and Image Processing Learning Resources

http://homepages.inf.ed.ac.uk/rbf/HIPR2/hipr_top.htm

Joy of Convolution

http://www.ysbl.york.ac.uk/~cowtan/fourier/fourier.html

http://www.ysbl.york.ac.uk/~cowtan/fourier/ftheory.html

ee5359_bme5300/2006spring/Signals & Systems Med-Img.pdf

http://www.prosig.com/signal-processing/FourierAnalysis.pdf

WEEK 3:

Linear System notes by Alavi.pdf

Fourier Transform Pairs by Poularikas and Seely.pdf

http://www.ysbl.york.ac.uk/~cowtan/fourier/fourier.html

http://www.ysbl.york.ac.uk/~cowtan/fourier/ftheory.html

http://www.eecs.umich.edu/~dnoll/BME516/ftnotes.pdf

http://www.eecs.umich.edu/~fessler/course/516/l/c2-linsys.pdf

ee4328-5339Spring12/Lec_Xray1Fe_05_04.pdf

ee4328-5339Spring12/Signals & Systems Med-Img.pdf

HOMEWORK 1 MedImSp12HW1.doc

ee4328-5339Spring12/Lec_Xray2Fe_10_04_.pdf

WEEK 4:EEK 4:

ee4328-5339Spring12/Lec_Xray2Fe_10_04_.pdf

ee4328-5339Spring12/LecXrayCT1_Fe_12_04.pdf

WEEK 5:

WEEK 5:

Black and white

ee4328-5339Spring12/LecXrayCT1_Fe_12_04_handouts.pdf

Color ee4328-5339Spring12/LecXrayCT1_Fe_12_04.pdf

ee4328-5339Spring12/Lec_XrayCT2Fe_17_04.pdf

http://www.aapm.org/meetings/02AM/pdf/8372-23331.pdf

MATLAB ASSIGNMENT Due Feb 21, 2012

Matlab_FFT_Exercise_1

Matlab_FFT_Exercise_2

WEEK 6:

MedImSp12HW2.doc

ee4328-5339Spring12/LecXrayCT3_Fe_19_04_.pdf

http://www.sv.vt.edu/xray_ct/parallel/Parallel_CT.html

ee4328-5339Spring12/FB.ppt

http://www.sv.vt.edu/xray_ct/parallel/Matlab_Prog.html

WEEK 7 and 8:

HW1_solution_MedIm

http://www.simplyphysics.com/IntroToMRI.html ******Find Narrative in http://www.simplyphysics.com/page2_1.html ******

Based on the above, another slide show MRI_Physics

www.mri-tutorial.com With Video below

http://sites.google.com/site/mritutorial/mri-physics-tutorials/1-video-intro-to-mri-physics/precession-and-resonance

Slide show http://fmri.ucsd.edu/ttliu/be280a_10/BE280A10_mri1.pdf

e-Book http://www.cis.rit.edu/htbooks/mri/inside.htm

Liely Chapter http://opax.swin.edu.au/~dliley/lectures/het408/mri.pdf

BME 595 J. D. Christensen MRI_1

http://en.wikibooks.org/wiki/Basic_Physics_of_Nuclear_Medicine/MRI_%26_Nuclear_Medicine

SlichterMagneticResonance.pdf

Slide 1(revised)

http://www.eecs.umich.edu/~fessler/course/516/l/cm-mri-1-33.pdf

http://opax.swin.edu.au/~dliley/lectures/het408/fbe.pdf

Sinogram in CT scan.pdf

Filtered Back Projection.pdf

4328_5339Sp12TH_EXAM_I

WEEK 9 and 10

ChoCh10.pdf

SlichterMagneticResonance.pdf

Slide 1(revised)

Resonance_SpinEchoSlide4(rev4)

Bloch equatios_Pulses_Fourier.pdf

WEEK 11

Slice Selection Gradient

http://www.revisemri.com/

http://www.revisemri.com/tutorials/

http://www.revisemri.com/questions/pulse_sequences/

http://www.mritutor.org/mritutor/pulseseq.htm

http://www.revisemri.com/questions/pulse_sequences/se_ge_differences

http://www.e-radiography.net/mrict/fund%20mr2/fundmri%202.htm T1, T2

http://eeweb.poly.edu/~yao/EL5823/MRI_instrumentation_ch13.pdf

http://www.imaios.com/en/e-Courses/e-MRI/

http://www.imaios.com/en/e-Courses/e-MRI/NMR

http://www.imaios.com/en/e-Courses/e-MRI/NMR/nuclear-spin

http://www.imaios.com/en/e-Courses/e-MRI/NMR/Precession-and-Larmor-frequency

http://www.imaios.com/en/e-Courses/e-MRI/NMR/Net-magnetization

http://www.imaios.com/en/e-Courses/e-MRI/NMR/Magnetic-Resonance

http://www.imaios.com/en/e-Courses/e-MRI/NMR/Excitation

http://www.imaios.com/en/e-Courses/e-MRI/NMR/Relaxation-nmr

http://www.imaios.com/en/e-Courses/e-MRI/MRI-signal-contrast

http://www.imaios.com/en/e-Courses/e-MRI/MRI-signal-contrast/Signal-recording

http://www.imaios.com/en/e-Courses/e-MRI/MRI-signal-contrast/90-RF-pulse

http://www.imaios.com/en/e-Courses/e-MRI/MRI-signal-contrast/180-RF-pulse

http://www.imaios.com/en/e-Courses/e-MRI/MRI-signal-contrast/Spin-echo-TR-TE

http://www.imaios.com/en/e-Courses/e-MRI/MRI-signal-contrast/TE-and-T2-weighting

http://www.imaios.com/en/e-Courses/e-MRI/MRI-signal-contrast/Signal-weighting **

http://www.imaios.com/en/e-Courses/e-MRI/MRI-signal-contrast/Tissue-contrast

http://www.imaios.com/en/e-Courses/e-MRI/Signal-spatial-encoding

http://www.imaios.com/en/e-Courses/e-MRI/Signal-spatial-encoding/Spatial-encoding-intro

http://www.imaios.com/en/e-Courses/e-MRI/Signal-spatial-encoding/Magnetic-field-gradients

http://www.imaios.com/en/e-Courses/e-MRI/Signal-spatial-encoding/Magnetic-field-gradients

http://www.imaios.com/en/e-Courses/e-MRI/Signal-spatial-encoding/Slice-select

http://www.imaios.com/en/e-Courses/e-MRI/Signal-spatial-encoding/Phase-encoding

http://www.imaios.com/en/e-Courses/e-MRI/Signal-spatial-encoding/Frequency-encoding

http://www.imaios.com/en/e-Courses/e-MRI/Signal-spatial-encoding/Interpreting-spatial-encoding-in-MRI

http://www.imaios.com/en/e-Courses/e-MRI/Signal-spatial-encoding/3D-spatial-encoding

http://www.imaios.com/en/e-Courses/e-MRI/The-Physics-behind-it-all

http://www.imaios.com/en/e-Courses/e-MRI/The-Physics-behind-it-all/Introduction

http://www.imaios.com/en/e-Courses/e-MRI/The-Physics-behind-it-all/Fourier-transform

http://www.imaios.com/en/e-Courses/e-MRI/The-Physics-behind-it-all/spatial-frequency

http://www.imaios.com/en/e-Courses/e-MRI/The-Physics-behind-it-all/2D-Fourier-transform

http://www.imaios.com/en/e-Courses/e-MRI/The-Physics-behind-it-all/K-space

http://www.imaios.com/en/e-Courses/e-MRI/The-Physics-behind-it-all/Gradients-and-spatial-frequency

http://www.imaios.com/en/e-Courses/e-MRI/The-Physics-behind-it-all/Spatial-frequency-image-contrast-and-resolution

http://www.imaios.com/en/e-Courses/e-MRI/MRI-Sequences

http://www.imaios.com/en/e-Courses/e-MRI/MRI-Sequences/MRI-sequences

http://www.imaios.com/en/e-Courses/e-MRI/MRI-Sequences/sequence-characteristics

http://www.imaios.com/en/e-Courses/e-MRI/MRI-Sequences/Sequence-classification

http://www.imaios.com/en/e-Courses/e-MRI/MRI-Sequences/Sequences-acronyms

http://www.imaios.com/en/e-Courses/e-MRI/MRI-Sequences/Spin-echo

http://www.imaios.com/en/e-Courses/e-MRI/MRI-Sequences/Fast-Spin-Echo

http://www.imaios.com/en/e-Courses/e-MRI/MRI-Sequences/Ultrafast-spin-echo

http://www.imaios.com/en/e-Courses/e-MRI/MRI-Sequences/inversion-recovery-stir-flair

http://www.imaios.com/en/e-Courses/e-MRI/MRI-Sequences/gradient-echo

http://www.imaios.com/en/e-Courses/e-MRI/MRI-Sequences/ultrafast-spoiled-gradient-echo

http://www.imaios.com/en/e-Courses/e-MRI/MRI-Sequences/steady-state-gradient-echo

http://www.imaios.com/en/e-Courses/e-MRI/MRI-Sequences/t2-enhanced-steady-state-gradient-echo

http://www.imaios.com/en/e-Courses/e-MRI/MRI-Sequences/balanced-gradient-echo

http://www.imaios.com/en/e-Courses/e-MRI/MRI-Sequences/echo-planar-imaging

http://www.imaios.com/en/e-Courses/e-MRI/MRI-Sequences/hybrid-echo

http://www.imaios.com/en/e-Courses/e-MRI/Improving-MRI-contrast-Imaging-water-and-fat

http://www.imaios.com/en/e-Courses/e-MRI/Improving-MRI-contrast-Contrast-agents

http://www.imaios.com/en/e-Courses/e-MRI/Improving-MRI-contrast-Contrast-agents/contrast-agents

How K-Space Works

How K-Space Works tutorial

WEEK 12

http://www.brooksidepress.org/Products/Military_OBGYN/Ultrasound/basic_ultrasound.htm

http://www.cs.sunysb.edu/~mueller/teaching/cse377/ultrasound.pdf

Application of Ultrasound in medicine:

http://en.wikipedia.org/wiki/Medical_ultrasonography

SwinburneUof Tech DavidLiley_ultrasound.pdf

SwinburneUof Tech DavidLiley_usisd.pdf

SwinburneUof Tech DavidLiley_doppler.pdf

http://web.eecs.umich.edu/~dnoll/BME516/us%20notes%201.pdf

http://web.eecs.umich.edu/~dnoll/BME516/us%20notes%202.pdf

WEEK 13

Introduction:

http://www.echo-web.com/secure/echo-202-free/echo202-1-body.asp?code=free

http://www.cs.sunysb.edu/~mueller/teaching/cse377/ultrasound.pdf

Ultrasound System (parameters, focusing, steering, and Math)

http://opax.swin.edu.au/~dliley/lectures/het408/usisd.pdf

Ultrasound.pptx

Ultrasound 2 _from D_Nol_l U _Mich.pptx

Beam formaing, Image formation

http://dukemil.bme.duke.edu/rsna07/RC632B.pdf

Doppler

http://radiographics.rsna.org/content/23/5/1315.full.pdf+html

Computed Ultrasound Tomography

http://www.cs.sunysb.edu/~mueller/teaching/cse377/US_09.pdf

http://www.cis.rit.edu/research/biomedical/ultrasoundintro/ultraintro.html

http://www.criticalecho.com/content/tutorial-1-basic-physics-ultrasound-and-doppler-phenomenon

http://www.criticalecho.com/content/tutorial-10-basic-physics-ultrasound-and-doppler-phenomenon

WEEK 14

http://www.cs.sunysb.edu/~mueller/teaching/cse377/nuclear.pdf

http://radiographics.rsna.org/content/15/4/975.full.pdf+html

http://radiographics.rsna.org/content/15/5/1179.full.pdf+html

http://radiographics.rsna.org/content/16/1/173.full.pdf+html

http://opax.swin.edu.au/~dliley/lectures/het408/radio.pdf

WEEK 15

ee4328-5339Spring12/Biomedical Imaging Applications of Light.pdf

http://www.drbio.cornell.edu/ApplicationNotes/SHG_Imaging_FvsB.pdf

Dr Dave OCT_module1.pdf

========================================

http://www.cis.rit.edu/htbooks/mri/

http://www.eecs.umich.edu/~fessler/course/516/index.html

http://fmri.ucsd.edu/ttliu/BE280A_10.html

http://engineering.dartmouth.edu/courses/engs167/

http://www.eecs.umich.edu/~dnoll/BME516/

http://opax.swin.edu.au/~dliley/lectures/het408/het408.html

http://opax.swin.edu.au/~dliley/lectures/het408/links.html

http://opax.swin.edu.au/~dliley/lectures/het408/backproj.pdf

http://www.cs.sunysb.edu/~mueller/teaching/cse377/mriImaging.pdf

http://www.cs.sunysb.edu/~mueller/teaching/cse377/

========================================

http://en.wikipedia.org/wiki/Radon_transform

http://mathworld.wolfram.com/RadonTransform.html

http://eivind.imm.dtu.dk/staff/ptoft/Radon/Radon.html

http://rsbweb.nih.gov/ij/plugins/radon-transform.html

http://www-math.mit.edu/~helgason/Radonbook.pdf

http://www.mathworks.com/help/toolbox/images/f21-25938.html

http://www.impactscan.org/slides/xrayct/

http://www.sprawls.org/resources/CTIMG/module.htm

http://www.physics.ubc.ca/~mirg/home/tutorial/fbp_recon.html

http://beige.ucs.indiana.edu/B673/node19.html ****

http://beige.ucs.indiana.edu/B673/node20.html

http://www.aapm.org/meetings/99AM/pdf/2806-57576.pdf

Magnetic Resonance Imaging:

http://fmri.ucsd.edu/ttliu/be280a_05/BE280A_05_mri4_3s.pdf

http://www.revisemri.com/

Medical Imaging SwinburneU.url [http://marr.bsee.swin.edu.au/~dtl/het408.html ]

http://www.mr-tip.com/serv1.php

http://www.mr-tip.com/serv1.php?type=db1&dbs=Pulse%20Sequence

http://www.ispub.com/journal/the_internet_journal_of_radiology/volume_2_number_1_55/article_printable/quantitative_magnetic_resonance_imaging_with_the_mixed_turbo_spin_echo_pulse_sequence_a_validation_study.html

http://www.chem.queensu.ca/facilities/nmr/nmr/webcourse/echo.htm

http://chem4823.usask.ca/hardware.html#Pulse

SwinburneDavidLiley_mri.pdf

http://chem4823.usask.ca/pulseseq.html

The Basics of MRI.url [ http://www.cis.rit.edu/htbooks/mri/inside.htm ]

http://rad.usuhs.mil/rad/handouts/fletcher/fletcher/

NMR-Slichter.pdf

T1 and T2 Weighting.doc

Magnetic Resonance Imaging Links

Herchel Smith Laboratory for Medicinal Chemistry, University of Cambridge Involved in the development of MRI technology and methods. Has a general introduction to MRI including some nice animations on the basis of frequency and phase encoding.
Basic Principles of MRI A basic introduction to MRI for a medically inclined audience
Basic Principles of MR Imaging Another nonmathematical introduction to MRI
The Basics of MRI An extremely comprehensive introduction to all aspects of magnetic resonance including spin physics, NMR spectroscopy, MRI and the relevant mathematics. Available in English, Italian and Russian. Highly recommended.
Functional MRI: Methods and Applications The PhD thesis by Dr Stuart Clare (University of Nottingham 1997). Contains useful information on fast imgaing sequences in particular the technique of echo planar imaging which is used in functional magnetic imaging.
Oxford Center for Functional Magnetic Resonance Imaging of the Brain
The Adelaide MRI Website Contains a lot of interesting information not found in the previous links like: MRI safety and links to equipment manufacturers.
Physics of MRI and two fast MRI techniques A nice paper written by a graduate student at MIT on the physics of MRI. If you are only interested in understanding the basis of MRI read the first part only. Moderately mathematical

Ultrasound Imaging:

http://www.indyrad.iupui.edu/public/lectures/physics/10ultras/

SwinburneUof Tech DavidLiley_ultrasound.pdf

SwinburneUof Tech DavidLiley_usisd.pdf

SwinburneUof Tech DavidLiley_doppler.pdf

http://dukemil.egr.duke.edu/Ultrasound/k-space/

http://fourier.eng.hmc.edu/e101/

http://fourier.eng.hmc.edu/e101/lectures/

http://fourier.eng.hmc.edu/e101/lectures/Image_Processing/

http://fourier.eng.hmc.edu/e101/lectures/Image_Processing/node6.html

http://en.wikipedia.org/wiki/Fourier_transform

http://www.cs.toronto.edu/~jepson/csc320/

http://www.cs.toronto.edu/~jepson/csc320/tutorials/matlabintro1.m

http://sepwww.stanford.edu/sep/prof/pvi/dft/paper_html/node17.html

http://sepwww.stanford.edu/sep/prof/pvi/dft/paper_html/node16.html

http://www.cs.unm.edu/~brayer/vision/fourier.html

http://www.cs.unm.edu/~brayer/vision/perception.html

http://cnyack.homestead.com/files/idxpages.htm

http://cnyack.homestead.com/files/artran/ft2dint1.htm

http://cnyack.homestead.com/files/artran/ft2dxy1.htm

19%20Nuclear%20Medicine.pdf

http://trshare.triumf.ca/~fretiere/TSI07/Talk/LecomteDay2.pdf

http://trshare.triumf.ca/~fretiere/TSI07/Talk/LecomteDay1b.pdf

http://trshare.triumf.ca/~fretiere/TSI07/Talk/LecomteDay1a.pdf

http://trshare.triumf.ca/~fretiere/TSI07/Talk/

http://www.eecs.umich.edu/~dnoll/BME516/

http://www.eecs.umich.edu/~dnoll/BME516/intro.pdf

http://www.eecs.umich.edu/~dnoll/BME516/ftnotes.pdf

http://www.eecs.umich.edu/~dnoll/BME516/us%20notes%201.pdf

http://www.eecs.umich.edu/~dnoll/BME516/us%20notes%202.pdf

http://www.eecs.umich.edu/~dnoll/BME516/us%20notes%203.pdf

http://www.eecs.umich.edu/~dnoll/BME516/ect.pdf

http://www.nap.edu/openbook.php?record_id=5066

http://www.eecs.umich.edu/~dnoll/BME516_04/

http://www.eecs.umich.edu/~fessler/course/516/index.html

http://www.eecs.umich.edu/~fessler/course/516/index.html

http://www.nap.edu/openbook.php?booksearch=1&term=Ultrasound&record_id=5066&bottom_Search+This+Book.x=35&bottom_Search+This+Book.y=31

That book formatted as a pdf file

The MRI chapter of that book

http://www.mathworks.com/academia/student_version/

http://www.eecs.umich.edu/~dnoll/BME516/us%20notes%202.pdf

http://farside.ph.utexas.edu/teaching/qm/lectures/lectures.html

http://farside.ph.utexas.edu/teaching/qm/lectures/node3.html

WEEK 10:

ChoCh10.pdf

NMR-Slichter.pdf

T1 and T2 Weighting.doc

WEEK 11:

How K-Space Works

How K-Space Works tutorial

SlichterMagneticResonance.pdf

http://farside.ph.utexas.edu/teaching/qm/lectures/node44.html

http://www.revisemri.com/tutorials/

http://www.revisemri.com/