60 http://www.imaginginformatics.ca/ en-us ℗ & © 20065 Imaging Informatics, University of Calgary Medical imaging research and in Stroke, Cancer and Multiple Sclerosis imaginginformatics.ca Imaging Informatics is a podcast of lectures about our research in imaging in the fields of Brain Cancer, Stroke, Multiple Sclerosis, Time/Frequency Analysis and Algorithms. Look for our Podcast in the iTunes Music Store Great advances have been made in medical imaging technology over the last two decades. Our podcast of lectures provides information about our medical imaging research into Brain Cancer, Stroke, Multiple Sclerosis, Algorithms and Time Frequency Anaylsis. http://www.imaginginformatics.ca/ Look for our Podcast in the iTunes Music Store. Mark Simpson zawada@bowfort.com Thorarin A Bjarnason PhD Defense Public Lecture, 2010.04.23 Quantitative T2 (qT2) is an emerging MRI field that utilizes the fundamental MRI T2 relaxation process and shows promise of being a non-invasive biomarker for myelin health. This thesis addresses a few limitations of qT2 understanding and analysis, including both a thorough examination of qT2 attributes that characterize more than just myelin health and improved methods of analysis. To begin, a thorough introduction of qT2 in terms of acquisition and analysis is presented, followed by a review of applications. Four studies of qT2 follow. The first study addresses qT2 analysis, presenting an open source, platform independent qT2 software package that works with data independent of MR manufacturer. A histology study follows. The next study addresses the optimal qT2 analysis method. Finally, noise is examined. Quantitative T2 analysis is best performed on data with Gaussian distributed noise, but MRI noise is Rician distributed and simulations show that Rician noise affects the T2 distribution. A temporal phase correction method is developed and applied to in vivo human and rat qT2 data to change the noise from Rician to Gaussian prior to performing qT2 analysis. http://podcasts.imaginginformatics.ca/20100423BjarnasonPublicLecture.m4v Thu, 19 May 2010 14:59:00 MDT 18:38 imaginginformatics, thorarin bjarnason, quantitative t2, qt2, mri, temporal phase correction, review, defense, phd, software, analyzennls, histopathology, multiple sclerosis Thorarin A Bjarnason, Tonima Ali, Mark Simpson, Cornelia Laule, J Ross Mitchell Presented at the Oxford Centre for Functional MRI of the Brain Seminar Series, Oxford University, 2009.10.26 T2 is commonly associated with different contrasts in MRI, which allows white and grey matter in brain to be visually separable as different shades of grey. By understanding the physics behind T2 we can use this relaxation mechanism to better characterize water within tissue. In this lecture I will briefly review the physics of T2 in order to highlight how it can be used as a contrast mechanism in MRI. A description of quantitative T2 (qT2) naturally follows, introducing the T2 distribution, which is a way of fully representing T2 relaxation times within an MR image. qT2 literature is reviewed, showing how different aspects of the T2 distribution reflect biology. For instance, short T2 times in the T2 distribution has been shown to correlate with myelin content, which could prove invaluable in monitoring neurodegenerative diseases such as multiple sclerosis (MS). Additionally, long T2 times in the T2 distribution highlights active lesions in MS patients. By fully characterizing the T2 relaxation process using MRI, T2 can be more than just a shade of grey. http://podcasts.imaginginformatics.ca/20091026BjarnasonOxford.m4v Tue, 15 Dec 2009 13:49:00 MDT 39:19 imaginginformatics, thorarin bjarnason, tonima ali, mark simpson, j ross mithcell, cornelia laule, quantitative t2, qt2, cancer, mri, temporal phase correction, review, multiple sclerosis Thorarin A Bjarnason, Tonima Ali, Mark Simpson, J Ross Mitchell, Cornelia Laule Presented at the Clark Smith Centre Common Research Meeting, University of Calgary, 2009.03.18 An introduction to MRI quantitative T2 (qT2) is presented along with applications to brain cancer. We begin by describing how MRI can be sensitive different water environments within a single pixel. We review histopathological validation of qT2 for measuring myelin and present recent findings of newly discovered water environments in various brain diseases. We finish off the presentation highlighting recent applications of qT2 in cancer and discuss our recent findings and research directions. http://podcasts.imaginginformatics.ca/200903qT2Cancer.m4v Thu, 14 May 2009 11:00:00 MDT 26:19 imaginginformatics, thorarin bjarnason, tonima ali, mark simpson, j ross mithcell, cornelia laule, quantitative t2, qt2, cancer, mri, background Thorarin A Bjarnason, J Ross Mitchell How to use AnalyzeNNLS, an opensource project from ImagingInformatics.ca. AnalyzeNNLS is designed to analyze multicomponent T2 decays from multiecho MRI experiments. This podcast provides a tutorial on how to use AnalyzeNNLS to analyze single-slice and multi-slice multiecho data. http://podcasts.imaginginformatics.ca/20081207AnalyzeNNLSTutorial.m4v Wed, 17 Dec 2008 14:15:00 MDT 10:37 qT2, T2 distribution, MRI, myelin, myelin water fraction, myelin water imaging, MRI, T2 relaxation, software, analyzennls, open source, thorarin bjarnason, j ross mitchell, tutorial Thorarin A Bjarnason, Tonima Ali, Mark Simpson, J Ross Mitchell Originally presented at the Advanced Imaging Seminar Series at the University of Calgary, 2008.11.20. Rerecorded for video podcast release. Quantitative T2 (qT2) has been shown to be sensitive to tissue microstructure in MRI. In particular, strong correlations have been found between myelin content and the area of peak with the shortest T2 time in the T2 distribution. The area of this short T2 peak is called the myelin water fraction. This video podcast outlines 3 main areas of Thorarin Bjarnason's PhD research to improve qT2. 1) Software: Thorarin Bjarnason has created opensource qT2 analysis software. More recently, Tonima Ali and Mark Simpson have been developing a qT2 visualization tool. 2) Workflows: Different workflows have been studied for qT2 analysis and we found that non-regularized multivoxel analysis is best suited for qT2. 3) Phase Correction: Phase correcting multiecho data changes the noise-type from Rician to Gaussian. Gaussian noise is preferred for qT2 analysis algorithms. http://podcasts.imaginginformatics.ca/20081201reAISS.m4v Wed, 20 Nov 2008 13:10:00 MDT 29:02 qT2, T2 distribution, MRI, myelin, myelin water fraction, myelin water imaging, MRI, T2 relaxation, regularization, software, analyzennls, open source, workflows, phase correction, thorarin bjarnason, tonima ali, mark simpson, j ross mitchell, lecture Thorarin A Bjarnason, Sylvia Drabycz, Mark Simpson, Ming Zhang, Tonima Ali, Mike Roberts, J Ross Mitchell Introduction to ImagingInformatics.ca research. Presented at the Welcome To SACRI Students Seminar, University of Calgary, 2008.10.17 An introduction to Medical Imaging Informatics and the current research of ImagingInformatics.ca. We outline 3D visualization and tissue characterization and the roles they are playing in virtual biopsy of brain cancer tumors. http://podcasts.imaginginformatics.ca/200810WelcomeStudentsMedicalImagingInformatics2.m4v Wed, 29 Oct 2008 07:01:00 MDT 20:22 Introduction to ImagingInformatics.ca research. Presented at the Welcome To SACRI Students Seminar, University of Calgary, 2008.10.17, Thorarin Bjarnason, Sylvia Drabycz, Mark Simpson, Ming Zhang, Tonima Ali, Mike Roberts, J Ross Mitchell Thorarin A Bjarnason, Cheryl R McCreary, Jeff F Dunn, J Ross Mitchell Presented at the Advanced Imaging Seminar Series, University of Calgary, 2008.02.21 Two common ways of performing qT2 analysis are to: 1) draw ROI, average T2 decays together, create T2 distribution, and 2) create T2 distributions for every pixel, draw ROI, average T2 distributions together. These two methods were compared and we determined that averaging T2 distributions together provides more accurate solutions than averaging T2 decay curves together. http://podcasts.imaginginformatics.ca/qT2WorkflowPodcast.m4a Mon, 14 Jul 2008 07:00:00 MDT 18:05 qT2, T2 distribution, MRI, myelin, myelin water fraction, myelin water imaging, MRI, T2 relaxation, regularization, smoothing, thorarin bjarnason, cheryl mccreary, jeff dunn, j ross mitchell, lecture Mark Simpson iiDicom Open Source Objective C and Python Dicom Imaging Framework On 1st November 2007, Mark Simpson presented the iiDicom Open Source Framework for Objective C and Python complete with code demonstrations. http://www.imaginginformatics.ca/open-source/ http://podcasts.imaginginformatics.ca/iiDicomFramework.m4v Thu, 01 Nov 2007 17:00:00 MDT 24:58 open source, dicom, medical imaging, quick dicom, quickdicom, objective c, python Thorarin A Bjarnason, Cornelia Laule, J Ross Mitchell Presented during a Multiple Sclerosis Joural Club Session, University of Calgary, 2007.03.09 An MR technique that quantifies white matter changes would be invaluable for following the pathological evolution of white matter diseases such as multiple sclerosis. Myelin water imaging is believed to quantify the amount of water trapped within the myelin bilayers inside white matter and has been proposed as a MR marker for myelin. The study outlined in this journal club presentation provides quantitative correlations of myelin water imaging and histopathology. Article: Laule C, Leung E, Li DKB, Traboulsee AL, Paty DW, MacKay AL, Moore GRW. "Myelin water imaging in multiple sclerosis: quantitative correlations with histopathology." 12:747-53 (2006). Presented: 2007.03.09. http://podcasts.imaginginformatics.ca/Myelin_Water_Imaging_and_Histopathology.m4b Wed, 21 March 2007 09:46:00 MDT 31:46 qT2, T2 distribution, MRI, myelin, myelin water fraction, myelin water imaging, histopathology, brain, MRI, multiple sclerosis, T2 relaxation, thorarin bjarnason, cornelia laule, j ross mitchell, lecture Thorarin A Bjarnason Presented at the Advanced Imaging Seminar Series, University of Calgary, 2007.01.06 Multiexponential analysis of MRI multiecho images (qT2) in healthy white matter generally provide three peaks in the T2 distribution. The shortest peak is believed to reflect myelin content. The final peak, often labeled cerebral spinal fluid, might result solely due to the noise characteristics of of magnitude data in some cases. A phase correction method is proposed that changes the noise characteristics from rician to gaussian appearing. When this method was applied to white matter regions of interest in 5 rats, the cerebral spinal peak disappeared. A more detailed study is required to study the effects on the remainder of the T2 distribution http://podcasts.imaginginformatics.ca/ComplexT2_2007_01_06.m4b Thu, 8 Feb 2007 14:45:00 MDT 19:06 qT2, T2 distribution, MRI, myelin, phase correction, thorarin bjarnason, lecture Dr. Ross Mitchell Presented at the ISAAC Workshop on Pseudo-Differential Operators: Partial Differential Equations and Time-Frequency Analysis at the Fields Institute, 2006.12.13 An overview of the Fourier-based medical imaging modalities of computerized tomography and magnetic resonance imaging are presented and several medical applications of time/frequency analysis are shown. Time/frequency techniques are used to investigate signals and images from patients suffering from stroke, brain cancer, multiple sclerosis, and epilepsy. Finally, applications of medical time/frequency algorithms extended for use on seismic signals for oil and gas discovery. We believe that time/frequency techniques have tremendous potential to advance the fields of science, engineering and medicine. Note: this presentation will be targeted towards a non-medical audience. Nevertheless, it may contain some graphic images. http://podcasts.imaginginformatics.ca/ISAAC_talk.m4b Thu, 8 Feb 2007 14:43:00 MDT 43:58 time/frequency, medical imaging, mitchell, ross, lecture Dr. Michael D. Hill Ischemic Stroke Thrombolysis and Brain Resucitation On 26th May 2006, Dr. Hill presented a lecture on Ischemic Stroke Thrombolysis and Brain Resuscitation. Slides are available for this lecture at http://www.imaginginformatics.ca/media/ http://podcasts.imaginginformatics.ca/MDHillLecture.m4v Fri, 26 May 2006 19:00:00 MDT 32:43 ischemic, stroke, thrombolysis, brain, resucitation, lecture Dr. Ross Mitchell An introduction to Time Frequency Analysis in Medical Images On 28th March 2006, Dr. Mitchell presented a lecture on time/frequency analysis of medical images for the PIMS/Shell Lunchbox Lecture Series. Slides are available for this lecture at http://www.imaginginformatics.ca/media/ http://podcasts.imaginginformatics.ca/PimsLecture280306.m4v Tue, 28 Mar 2006 19:00:00 MDT 48:10 time, frequency, shell, mitchell, ross, lecture