Beauchamp:Teaching

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[[Beauchamp:TeachingOld|Archive of Previous Teaching Page]]
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<h3>Courses</h3>
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==Learning more about Neuroimaging==
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To learn more about neuroimaging, consider the two course sequence taught by David Ress and Michael Beauchamp at Baylor College of Medicine.
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===Fundamentals of Human Neuroimaging===
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The first course in the sequence, taught in the Fall (Terms 1 and 2) is directed by David Ress. It is primarily a lecture course survey of neuroimaging methods and results. In 2014, the course was offered on Tuesdays and Thursdays from 10:50am to 12:05 pm. The course schedule may change in the future, please contact Dr. Ress for schedule information. This course is listed as a BCM course (GS-NE-400) and is cross-listed at Rice as NEUR 430.
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Goals and learning objectives:
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#Develop familiarity with basic neuroanatomy and electrophysiology.
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#Understand the physical basis of magnetic resonance imaging of tissue structure, including the nuclear magnetic resonance, contrast mechanisms, image acquisition, signal processing, and scanner hardware.
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#Understand the physiology of neurovascular coupling, and explore its effects on both optical signals and MRI.
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#Understand basic concepts, hardware, and analysis of positron emission tomography.
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#Become familiar with neuroscience imaging experiment design, analysis, and results, particularly as they are applied human vision science.
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Neuroscience elective. 3 Credits for 2 terms (Terms 1 and 2). T/Th. Prerequisites: Introductory Calculus and Physics at the freshman level.
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Course director: David Ress, Ph.D.
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NBA Seminar Series Available Dates:
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===Advanced Functional Magnetic Resonance Imaging Laboratory===
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[[Beauchamp:AvailableDates20142015|Available Dates for 2014 - 2015]]
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The second course in the sequence, taught in the Spring, is directed by Michael Beauchamp, course director. The course is listed as BCM GS-NE-472 (350-472) and is cross-listed as Rice Psychology 585. This is a limited enrollment course focussed on practical MRI techniques. Students will collect and analyze MRI data. The course is designed for graduate students, fellows, and others actively collecting MRI data for a research project. The course is typically taught on Wednesdays from 9am to 11:30am. This is a 2 credit course with Pass/Fail grading. The prerequisite is completion of the first course in the sequence, GS-NE-400 (above) and permission of instructor. The course is taught in Term 4. In 2016, the dates for this term are March 14 - May 13, 2016 (last class day May 6).
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#3/16/16 CAMRI Safety Training (if not already completed). 10 - 10:45, CAMRI Conference Room.
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#3/23/16  fMRI Data Analysis Part I: Block Design
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#3/30/16  fMRI Data Analysis Part 2: Event-Related Design
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#4/6/16  Hands-On Dataset Analysis Introduction to data6
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download all afni_data datasets from
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https://afni.nimh.nih.gov/pub/dist/edu/data/
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work through handouts at
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https://afni.nimh.nih.gov/pub/dist/edu/latest/
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#4/13/16 Further Analysis of data6. afni06_decon.ppt NB: this uses the data in the afni_data2 folder.
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#4/20/16  AFNI Boot Camp in Tulsa, OK. Demo of Flywheel Data Management System.
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#4/27/16  Intro to DTI with Paul Taylor, contents TBD
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#5/4/16 Skype Class on Freesurfer
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General information about UT courses is available at  https://my.uth.tmc.edu
 
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GS14 1181: Graduate Neuroanatomy
 
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Fall/annually/1-credit hour course. The Graduate Neuroanatomy course will provide a broad overview of the structure and function of the central nervous system. The general architecture of the nervous system and its functional systems are presented in a series of online exercises. The exercises allow the students to examine brain anatomy at a detailed view of the regional anatomy of the brain and spinal cord. MRIs of brain anatomy, as commonly presented in the scientific literature, will be presented using a computerized learning system. [[Beauchamp:GraduateNeuroanatomy|Click here for web page for Graduate Neuroanatomy Course]]
 
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====Course Details====
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<h4>2012</h4>
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Students will need to take an MRI safety course offered by CAMRI.
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Here are slides presented in June 2012 at the Institute of Psychology of the Chinese Academy of Sciences
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#[[media:BeijingJune2012.pdf.pdf|Institute of Psychology of the Chinese Academy of Sciences]]
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Here are slides presented for Medical Neuroscience in 2012
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#[[media:2012Integrated.pdf|Integrated Motor Systems]]
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#[[media:2012MotorCortex.pdf|Motor Cortex]]
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#[[media:2012SpinalCord.pdf|Spinal Cord]]
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#[[media:2012PreLab8.pdf|Prelab slides for Lab #8]]
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#[[media:2012PreLab9.pdf|Prelab slides for Lab #9]]
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Click here for [[Beauchamp:MedNSLab|Teaching Material for Medical Neuroscience Laboratory Course]]
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UT Graduate Cognitive Neuroscience (Anne Sereno, course director)
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#[[media:SerenoLecture1.pdf|Lecture #1, Methods of Cognitive Neuroscience]]
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#[[media:SerenoLecture2.pdf|Lecture #2, Object Recognition]]
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<h4>2011</h4>
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BCM Higher Brain Function (Mariela DeBiasi, course director)
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#[[media:DeBiasiLecture1.pdf|Lecture #1]]
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#[[media:DeBiasiLecture2.pdf|Lecture #2]]
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#[[media:fMRIEducatedConsumer.pdf|fMRI Educated Consumer Slides]]
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#[[Beauchamp:WUES|Information about West U Elementary School Science Night]]
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#[[media:BasalGanglia.ppt|Basal Ganglia MRI Slides for "crowdsource" labeling]]
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Here are slides presented for Medical Neuroscience in 2011
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#[[media:2011Lecture1.pptx|Neuroimaging]]
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#[[media:2011MotorLecture1.pdf|Motor System Lecture #1]]
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#[[media:2011MotorLecture2.pdf|Motor System Lecture #2]]
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#[[media:2011MotorLecture3.pdf|Motor System Lecture #3]]
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#[[media:2011MotorLecture4.pdf|Motor System Lecture #4]]
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#[[media:2011MotorLecture5.pdf|Motor System Lecture #5]]
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#[[media:2011MotorLecture6.pdf|Motor System Lecture #6]]
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#[[media:2011PreLab8.pdf|Prelab slides for Lab #8]]
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#[[media:2011PreLab9.pdf|Prelab slides for Lab #9]]
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<h5>2011 Lab 7 Notes</h5>
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The NeuroLab CD contains incorrect information on the location of the frontal eye fields. This PDF shows the correct location
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[[media:Lab7FrontalEyeFields.pdf|FrontalEyeFields]]
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<h5>2011 Lab 8 Notes</h5>
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Many of the structures in Lab 8 can be seen on MRI. The following PDF contains labeled MRI sections.
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[[media:Lab8MRI.pdf|Lab8MRI]]
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<h5>2010 Lecture Slides</h5>
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Here are slides presented for Introduction to Neuroimaging on January 22, 2010
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[[media:2010Lecturev2.pptx|Neuroimaging]]
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Here are slides presented for Motor System Lecture #1 (muscles) on March 17, 2010
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[[media:Lecture1.pptx|Motor Systems Lecture #1]]
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Here are slides presented for Motor System Lecture #2 (spinal reflexes) on March 17, 2010
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[[media:Lecture2.pptx|Motor Systems Lecture #2]]
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Here are slides presented for Motor System Lecture #3 (motor cortex) on March 19, 2010
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[[media:Lecture3.pptx|Motor Systems Lecture #3]]
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Here are slides presented for Motor System Lecture #4 (basal ganglia) on March 22, 2010
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[[media:Lecture4.pptx|Motor Systems Lecture #4]]
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Here are slides presented for Motor System Lecture #5 (cerebellum) on March 24, 2010
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[[media:Lecture5.pptx|Motor Systems Lecture #5]]
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Here are slides presented for Prelab #9 (descending pathways) on March 29, 2010
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[[media:PreLab9.pptx|Prelab #9]]
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<h5>Other Notes</h5>
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A teaching website that shows midbrain, brainstem and spinal cord slices labeled with tracts and anatomy is
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http://isc.temple.edu/neuroanatomy/lab/
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A website that shows labeled brain anatomy from the Visible Human project is
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http://www.netanatomy.com
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A free iPhone app from the Cold Spring Harbor Laboratory allows 3D visualization of brain structures
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http://itunes.apple.com/us/app/3d-brain/id331399332?mt=8
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A web-based version of the same app may be seen at
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http://www.g2conline.org/
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misc teaching notes:
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[[Beauchamp:MedNSLabNotes]]
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<h4>MS4 Neuroimaging Elective: BSCI 4008</h4>
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[[Beauchamp:NeuroimagingElective|Web page for fourth-year neuroimaging elective]]
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==AFNI/fMRI Short Course==
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Dr. Bob Cox, the Director of the Scientific and Statistical Computing Core at the National Institute of Mental Health Intramural Research Program will be visiting Houston on October 4-8, 2010. Together with his staff, Dr. Cox will teach a 5-day course on fMRI data analysis with the AFNI software package.
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[[Beauchamp:ShortCourse2010|Click for more information on the short course]]
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==Introduction to fMRI==
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Students will need to take an MRI safety course. Krista Runge will offer one on Sept 18 at 1 p.m., or will offer one specially for students in the class if that time is not convenient.
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The web page for students in this course to submit assignments and receive information about the course is
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https://owlspace-ccm.rice.edu/portal
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For Fall 2014 - Spring 2015, this course will be offered on Wednesday mornings from 9 am to 11:30 am in UT MSB B.625
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The first class will be Wednesday September 3 and the last class will be Wednesday December 10th. There will be no class on November 19th (Society for Neuroscience annual meeting) or November 26th (Thanksgiving Holiday). In general, the course follows the schedule of the UT GSBS.
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https://gsbs.uth.edu/current-students/academics/academic-calendar/index.htm
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Tentative course schedule
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Class # Class Date Class Topic
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1 9/3/14 1. Safety Briefing  2. Collect Block Design fMRI data
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2 9/10/14 1. Install AFNI on Mac or Linux computers.  2. Analyze Block design fMRI data from class #1
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3 9/17/14 Collect Event Related fMRI data
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4 9/24/14 Analyze Event Related fMRI data
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5 10/1/14 Collect single subject anatomical (T1) data
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6 10/8/14 Analyze anatomical data: create Cortical Surface model using Free Surfer
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7 10/15/14 Collect Group fMRI and structural data
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8 10/22/14 Analyze Group fMRI data
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9 10/29/14 Analyze Group structural data (VBM)
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10 11/5/14 Collect resting state fMRI data TBD (MSB at NIH SPC study section)
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11 11/12/14 Analyze resting state fMRI data
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11/19/14 No Class (Society for Neuroscience annual meeting)
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11/26/14 No Class (Thanksgiving holiday)
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12 12/3/14 Collect pulse sequence comparison data (EPI vs. spiral)
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13 12/10/14 Analyze pulse sequence comparison data
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This course is intended for graduate students, post-doctoral fellows and faculty who are interested in using fMRI for their research. A small number of undergraduates may also enroll in the course solely at the discretion of the instructor (only undergraduates who are currently working in a laboratory that uses functional MRI study will be considered). The course is primarily offered through the University of Texas Graduate School of Biomedical Sciences GSBS 140053 (http://www.uthouston.edu/gsbs/current-students/academics/course-listing/courses/neuroscience/gs140053-introduction-to-functional-magnetic-resonance-imaging-.htm). The course is also cross-listed at Rice University in the Psychology and Bioengineering departments (as Psych 579 and BioE 571) and in the Baylor College of Medicine Graduate School of Biological Sciences (as GS-NE-439) (http://neuro.bcm.edu/?sct=neuro_think&gp=cdescript). If you are a student at UT, Rice or Baylor contact your registrar for enrollment information.
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If you are a student at University of Houston, it is probably easiest to enroll in the course via cross-registration through Rice University. (UT requires vaccination records for cross-registration which is annoying). However, if you would like to enroll through UT, please visit this web page for information about enrolling in the course:
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http://registrar.uth.tmc.edu/Registration/ConcurEnrollment.html
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The textbook for this course is "Functional Magnetic Resonance Imaging", <b>2nd edition</b>, by Huettel, Song and McCarthy.
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The text may be ordered from Amazon
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http://www.amazon.com/Functional-Magnetic-Resonance-Imaging-Second/dp/0878932860
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or it is available at the UT bookstore at a 10% discount. For more information on the UT bookstore:
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  https://www.webmedbooks.com/uthouston/content/contact.aspx
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After Fall 2014, the course will undergo substantial renovation. It will be renamed "Fundamentals of Human Neuroimaging" and split into two parts that will be offered in the Fall and Spring of every year.
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Dr. David Ress will teach the first part, primarily a lecture course on basic principles. Dr. Beauchamp will teach the second part, primarily a lab course on applied fMRI techniques.
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#Spring 2015: no fMRI course
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#Fall 2015: Ress teaches part I (more theoretical)
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#Spring 2016: Beauchamp teaches part II (more practical)
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#Repeat for each following Fall/Spring
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<h4>Other Courses and Lectures</h4>
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A second course offered by Dr. Beauchamp is titled "Advanced Seminars in Neuroimaging". This is an advanced course for students who have already taken Introduction to fMRI.
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Click here for information about a lecture on fMRI delivered at Texas Children's Hospital on December 2nd, 2009:
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[[Beauchamp:TCH|TCH Lecture]]
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A GSBS course on MRI physics is shown here
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http://www.uthgsbsmedphys.org/GS02-0193/default_2009.htm
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[[media:IUTalk.pdf|Lecture at Indiana University in February of 2004]]
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Writing Courses:
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Picus,Mark A <MAPicus@mdanderson.org> offers a summer course Writing Scientific Articles for Publication (GS21-1142).
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Current revision

Brain picture
Beauchamp Lab


Archive of Previous Teaching Page

Contents

Learning more about Neuroimaging

To learn more about neuroimaging, consider the two course sequence taught by David Ress and Michael Beauchamp at Baylor College of Medicine.

Fundamentals of Human Neuroimaging

The first course in the sequence, taught in the Fall (Terms 1 and 2) is directed by David Ress. It is primarily a lecture course survey of neuroimaging methods and results. In 2014, the course was offered on Tuesdays and Thursdays from 10:50am to 12:05 pm. The course schedule may change in the future, please contact Dr. Ress for schedule information. This course is listed as a BCM course (GS-NE-400) and is cross-listed at Rice as NEUR 430. Goals and learning objectives:

  1. Develop familiarity with basic neuroanatomy and electrophysiology.
  2. Understand the physical basis of magnetic resonance imaging of tissue structure, including the nuclear magnetic resonance, contrast mechanisms, image acquisition, signal processing, and scanner hardware.
  3. Understand the physiology of neurovascular coupling, and explore its effects on both optical signals and MRI.
  4. Understand basic concepts, hardware, and analysis of positron emission tomography.
  5. Become familiar with neuroscience imaging experiment design, analysis, and results, particularly as they are applied human vision science.

Neuroscience elective. 3 Credits for 2 terms (Terms 1 and 2). T/Th. Prerequisites: Introductory Calculus and Physics at the freshman level. Course director: David Ress, Ph.D.

Advanced Functional Magnetic Resonance Imaging Laboratory

The second course in the sequence, taught in the Spring, is directed by Michael Beauchamp, course director. The course is listed as BCM GS-NE-472 (350-472) and is cross-listed as Rice Psychology 585. This is a limited enrollment course focussed on practical MRI techniques. Students will collect and analyze MRI data. The course is designed for graduate students, fellows, and others actively collecting MRI data for a research project. The course is typically taught on Wednesdays from 9am to 11:30am. This is a 2 credit course with Pass/Fail grading. The prerequisite is completion of the first course in the sequence, GS-NE-400 (above) and permission of instructor. The course is taught in Term 4. In 2016, the dates for this term are March 14 - May 13, 2016 (last class day May 6).

  1. 3/16/16 CAMRI Safety Training (if not already completed). 10 - 10:45, CAMRI Conference Room.
  2. 3/23/16 fMRI Data Analysis Part I: Block Design
  3. 3/30/16 fMRI Data Analysis Part 2: Event-Related Design
  4. 4/6/16 Hands-On Dataset Analysis Introduction to data6

download all afni_data datasets from https://afni.nimh.nih.gov/pub/dist/edu/data/ work through handouts at https://afni.nimh.nih.gov/pub/dist/edu/latest/

  1. 4/13/16 Further Analysis of data6. afni06_decon.ppt NB: this uses the data in the afni_data2 folder.
  2. 4/20/16 AFNI Boot Camp in Tulsa, OK. Demo of Flywheel Data Management System.
  3. 4/27/16 Intro to DTI with Paul Taylor, contents TBD
  4. 5/4/16 Skype Class on Freesurfer


Course Details

Students will need to take an MRI safety course offered by CAMRI.

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