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My Mathematics 597 page
Summer 2008 course at California State University, Fullerton

Nasser M. Abbasi

Summer 2008   Compiled on November 24, 2018 at 12:25am  [public]

Contents

1 Introduction
 1.1 Class description
2 Reports
 2.1 HYPR simulator software
 2.2 Midterm group presenations
  2.2.1 HYPR presentation
  2.2.2 Level set report
 2.3 Final group presenations
  2.3.1 Final HYPR presentation
  2.3.2 W-Hypr presenations
 2.4 Different team members writings
  2.4.1 Current Status of HYPR Computational Investigation By Doug
  2.4.2 MLEM vs. HYPR by Doug
  2.4.3 MLEM vs HYPR By Theory group
  2.4.4 Computational results By Theory group
  2.4.5 GP597 report By Hassan
  2.4.6 HYPER report By Hassan
3 My project notebook
4 My report on effect of using sliding window for HYPR
5 Matlab functions and simulation
6 Class handouts and reference papers
7 Link

1 Introduction

This course part of my Masters degree in Applied Mathematics at California State University, Fullerton.

pict

Figure 1: class schedule

1.1 Class description

course˙description.pdf

2 Reports

2.1 HYPR simulator software

Matlab program I wrote for the project is here

2.2 Midterm group presenations

2.2.1 HYPR presentation

HYPRReport˙6˙23˙08.pdf

2.2.2 Level set report

LevelSetReport˙6˙23˙08.pdf

2.3 Final group presenations

2.3.1 Final HYPR presentation

HYPR-7-21-08final.pdf

2.3.2 W-Hypr presenations

w-hypr.pdf

2.4 Different team members writings

2.4.1 Current Status of HYPR Computational Investigation By Doug

stangCurrent˙Status˙of˙HYPR˙Computational˙Investigation.pdf

2.4.2 MLEM vs. HYPR by Doug

mlemsection.pdf

2.4.3 MLEM vs HYPR By Theory group

MLEM˙HYPR.pdf

2.4.4 Computational results By Theory group

stanginput.pdf

2.4.5 GP597 report By Hassan

GP597.pdf

2.4.6 HYPER report By Hassan

HYPER.pdf

3 My project notebook

progress.pdf

4 My report on effect of using sliding window for HYPR

index.pdf

5 Matlab functions and simulation

This section will contain collection of functions and simulation I made during work on this project.

  1. M file to generate a disk of some radius and center. added June 9, 2008. This function returns a 2D matrix of a disk (white=1,black=0) nma_makeDisk.m

  2. This file is a driver for the above function. Shows examples of how to call the function nma_driver_makeDisk.m

6 Class handouts and reference papers





# date

handout description

link





1 Tuesday 5/27/2008

Paper: Highly Constrained Backprojection for Time-Resolved MRI by C. A. Mistretta, O. Wieben, J. Velikina, W. Block, J. Perry, Y. Wu, K. Johnson, and Y. Wu1

link





2 Tuesday 5/27/2008

Paper: Iterative projection reconstruction of time-resolved images using highly-constrained back-projection (HYPR) by Rafael L. O’Halloran, Zhifei Wen, James H. Holmes, Sean B. Fain

link





3 Tuesday 5/27/2008

Paper: Level Set Reconstruction for Sparse Angularly Sampled Data by Sungwon Yoon; Pineda, R.; Fahrig, R.

link





4 Tuesday 5/27/2008

Paper: Reconstructing absorption and diffusion shape profiles in optical tomography by a level set technique by M. Schweiger, S. R. Arridge, O. Dorn, A. Zacharopoulos, and V. Kolehmainen

link





5 Tuesday 5/27/2008

3 pages from book, on discretization delimma

PDF





6 Tuesday 5/27/2008

3 pages from book Foundations of Image Science on MLEM algorithm

PDF





7 Thursday 5/29/2008

Tomographic Image Reconstruction Derivation of the central slice theoreom

link





8 Thursday 6/5/08

Professor’s Gearhart Derivation of Equation (7) in the paper by Sungwon Yoon, A Pineda, and R. Fahrig

PDF





9 Monday 6/9/08

Paper (Wright- Huang -HYPR) Time-Resolved MR Angiography With Limited Projections Yuexi Huang and Graham A. Wright

PDF





10 Monday 6/9/08

PPT presentation of HYPR by GE

PDF





11 Wed 6/12/08

Scan of page from Kak/Stany showing analytical solution to projection of ellipes

image





12 Monday 6/16/08

Paper: Improved Waveform Fidelity Using Local HYPR Reconstruction (HYPR LR) by Kevin M. Johnson, Julia Velikina,Yijing Wu,Steve Kecskemeti,Oliver Wieben, and Charles A. Mistretta

PDF





13 Thursday 6/19/08

The EM algorithm handout given to us by Dr Gearhart

PDF





14 Thursday 6/19/08

Handout from Dr Pineda, the goals of the HYPR project

PDF





15 Thursday 6/26/08

Siavash Jalal write up on EM

PDF





16 Wed 7/02/08

Paper: Projection Reconstruction MR Imaging Using FOCUSS Jong Chul Ye, Sungho Tak, Yeji Han, and Hyun Wook Park

PDF





17 Wed 7/02/08

Paper: An Application of Highly Constrained Backprojection (HYPR) to Time-Resolved VIPR Acquisition J. V. Velikina1, C. A. Mistretta1, K. M. Johnson1, O. Wieben1

PDF





18 Tuesday 7/8/08

Talk by Jeff Fessler at SIAM 2008 in San Diego on MRI

PDF





19 Thursday 7/10/08

Send to us by Dr Pineda: Paper Evaluation of Temporal and Spatial Characteristics of 2D HYPR Processing Using Simulations by Yan Wu, Oliver Wieben, Charles A. Mistretta, and Frank R. Korosec

PDF





20 Sunday 7/12/08

Paper: Time-Resolved Contrast-Enhanced 3D MR Angiography by Frank R. Korosec, Richard Frayne, Thomas M. Grist, Charles A. Mistretta

PDF





21 Sunday 7/12/08

Paper: MAGNETIC RESONANCE IMAGING (MRI) SIMULATION ON A GRID COMPUTING ARCHITECTURE H. BENOIT-CATTIN, F. BELLET, J. MONTAGNAT, C. ODET

PDF





22 Sunday 7/12/08

Thesis: Multidimensional MRI of Cardiac Motion Acquisition, Reconstruction and Visualization Andreas Sigfridsson LIU-TEK-

PDF





23 Monday 7/12/98

Siavash derivation of SNR for HYPR

PDF





24 Sunday 7/19/08

from Doug, MLEM related power points. Mathematical relation of MLEM to HYPR

PDF





25 Tuesday 7/22/08

Paper A self referencing level set method for image reconstruction 2002

PDF





26 Saturday 7/26/08

Paper: 3D Time-Resolved Contrast-Enhanced Cerebrovascular MR Angiography with Subsecond Frame Update Times Using Radial k-Space Trajectories and Highly Constrained Projection Reconstruction Y. Wu, N. Kim, F.R.

PDF





27 Sunday 7/27/08

Paper: Undersampled Radial MRI with Multiple Coils. Iterative Image Reconstruction Using a Total Variation Constraint by Kai Tobias Block, Martin Uecker, and Jens Frahm

PDF





28 Sunday 7/27/08

Paper: Radial Single-Shot STEAM MRI By Kai Tobias Block and Jens Frahm

PDF





29 Sunday 7/27/08

Paper: Novel Radial MRI Technique for Obtaining High Resolution Black Blood Images of the Heart with and without Fat Suppression from a Single k-space Data Set by Zhiqiang Li, Ali Bilgin, Arthur F. Gmitro, and Maria . Altbach1

PDF





30 Friday 8/15/08

Paper: HYPRIT: Generalized HYPR Reconstruction by Iterative Estimation Samsonov AA, Wieben O, Block WF.

PDF





31 Friday 8/15/08

Paper: More Optimal HYPR Reconstructions Using a Combination of HYPR and Conjugate-Gradient Minimization by M. A. Griswold1, K. Barkauskas, M. Blaimer, J. L. Sunshine, and J. L. Duerk

PDF





7 Link

  1. urlhttp://scien.stanford.edu/class/psych221/projects/02/insomnia/ NOISE measurements in MRI (SNR) and matlab code
  2. http://visielab.ua.ac.be/staff/sijbers/snr_ref.html web page of references on SNR in MRI
  3. http://www.eng.warwick.ac.uk/oel/courses/undergrad/lec13/applications.htm 3. http://www.eng.warwick.ac.uk/oel/courses/undergrad/lec13/applications.htm good notes on MRI andbackprojection in general. Warick univ. England.
  4. http://www.patentstorm.us/patents/7277597/description.html talk about radial acquiztion.
  5. http://www.impactscan.org/slides/eanm2002/sld001.htm on Filtered backprojection and CT
  6. http://www.eecs.umich.edu/~fessler/ Dr John Fessler web page. He does MRI and this page contains software and papers. The link below is MRI data found on this page.
  7. http://www.nap.edu/readingroom/books/biomedical/ on-line medical imaging book Mathematics and Physics of Emerging Biomedical Imaging
  8. http://www.eecs.umich.edu/~fessler/course/516/a/books.txt Dr Fessler recommended books on medical imaging.
  9. http://www.eecs.umich.edu/~fessler/result/mr/angio/ MRI data. This is from Fessler group.
  10. http://www.radiology.mcg.edu/radiologyphysics/mri/MR%20cha8%20SNR.ppt very good PPT on MRI
  11. http://www.radiology.mcg.edu/radiologyphysics/ Where the above was taken. (the chp4 one is GOOD) also the k-space one
  12. http://www-cellbio.med.unc.edu/henson_mrm/ looks like have MRI data here. Check it out
  13. http://www.ehealthmd.com/library/mri/MRI_whatis.html good description of how MRI works, but no pictures.
  14. http://www.mabot.com/brain/ some brain MRI images
  15. http://www.hull.ac.uk/mri/lectures/gpl_page.html intro to MRI
  16. http://www.sph.sc.edu/comd/rorden/mritut.html MRI tutorial and nice software. Download software to my references folder for math 597 csuf and tried it. No more time.
  17. http://www.fonar.com/glossary.htm MRI glossary
  18. http://dnl.ucsf.edu/users/dweber/dweber_docs/mri_quality.html good page on MRI quality
  19. http://www.dimag.com/cardiovascular/journal/showArticle.jhtml?articleID=201202400 good discussion on sampling for imaging
  20. http://airto.bmap.ucla.edu/BMCweb/SharedCode/SpeedLimit/SpeedLimit.html good article on MRI
  21. http://www.bic.mni.mcgill.ca/cgi/bw/submit_request MRI simulation data request. I did it, but no reply.
  22. http://www.nitrc.org/projects/pediatric_mri/ MRI data
  23. http://www.bic.mni.mcgill.ca/nihpd/info/data_access.html data access
  24. http://mipav.cit.nih.gov/download.php some MRI application, requires Java stuff.
  25. http://www.e-mri.org/quality-artifacts/signal-to-noise-ratio.html SNR for MRI
  26. http://dynamo.ecn.purdue.edu/~bouman/software/tomography/ MRI matlab data
  27. http://en.wikipedia.org/wiki/Projection-slice_theorem Central slice theorem
  28. http://www.slaney.org/pct/ Book Principles of Computerized Tomographic Imaging. See chapter 7. Here is the web page of the book which can be downloaded for free or buy from amazon by Avinash C. Kak and Malcolm Slaney
  29. http://www.archive.org/details/Lectures_on_Image_Processing on-line lectures on digital image processing.
  30. http://www.ismrm.org/ The International Society for Magnetic Resonance in Medicine
  31. http://www.ismrm.org/07/Session53.htm This page contains papers on Compressed Sensing and HYPR (It is part of workshop by ISMRM held in 2007)
  32. http://www.cs.ubc.ca/~mitchell/ToolboxLS/ Level set Matlab toolbox (thanks to Dr Pineda for the link)
  33. http://focus.ti.com/docs/solution/folders/print/275.html contains a detailed block diagram of MRI