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Neuroimaging

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ncp:ncpcourse1819 [2018/10/22 14:18] – [Session titles] vflanaginncp:ncpcourse1819 [2018/11/10 12:08] (current) – [Visit to the MRI machine] vflanagin
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 ==== Time and schedule ==== ==== Time and schedule ====
  
-|Date and time: |Mondays 10:15 a.m. (10:00 a.m. if you have questions |+|Date and time: |Mondays 10:15 a.m. (10:00 a.m. for anyone wishing to ask questions) |
  
   * Part 1: MR physics (Virginia Flanagin)   * Part 1: MR physics (Virginia Flanagin)
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-==== Summary ====   +==== Summary & Objectives ====   
-An introduction to the theory and practice of functional and structural neuroimaging, with a combination of lectures, hands on experience with MRI, and data analysis methods including: functional magnetic resonance imaging (fMRI), morphometry and structural imaging including diffusion tensor imaging, simultaneous electroencephalography (EEG), and data analysis with e.g. SPM12. This is a unique opportunity to get to know the newest techniques in the field of neuroimaging, and learn about the type of research that is being done in this area in a number of different faculties around Munich.+This course provides an introduction to the theory and practice of magnetic resonance imaging (MRI), in particular functional magnetic resonance for the masters program in Neuro-cognitive Psychology (NCP). It consists of a combination of lectures, a trip to the MRI and data analysis methods. We will focus on the data acquisition and analysis of fMRI data. 
 + 
  
 +The course is set up as 1.5 hours of lecture in the morning. Because the content of the course builds on previous lessons, the lecture portion will be split-up into a review followed by the current week's lesson. 
  
 +In the last part of the course, you will also have tutorials, these will be longer than the lecture part of the course. 
 +
 +
 +
 +== Learning Objectives ==
 +At the end of this course, students should be able to:
 +
 +  * Work safely in an MRI environment
 +  * Identify artefacts in MRI data and describe their causes based upon MR physics
 +  * List the steps to prepare MRI data for scientific analysis
 +  * Correctly design an fMRI study
 +  * Perform a basic fMRI analysis using the toolbox Statistical Parametric Mapping (SPM) (version 12) for Matlab
 +  * Critically evaluate the methods section of scientific papers that use fMRI
 +  
 ==== Visit to the MRI machine ==== ==== Visit to the MRI machine ====
  
-  * Please sign-up for your preferred time slots to visit the MRI machine here+  * Slot 1: 16.11.2018 at 12:00 - 13:30 
 +  * Slot 2: 16.11.2018 at 15:30 - 17:00 
 +   
 + 
 + 
 +== Directions to the MRI machine == 
 +  * The Prisma is in the basement of the Institute for Stroke and Dementia (ISD), Feodor-Lynen-Str. 17 in Munich 
 +  * Walking directions from the subway (exit at the front of the train from the city): [[https://www.google.de/maps/dir/Marchioninistra%C3%9Fe,+81377+M%C3%BCnchen/LMU+-+Institut+f%C3%BCr+Schlaganfall-+und+Demenzforschung/@48.1137593,11.4672233,16z/data=!4m14!4m13!1m5!1m1!1s0x479dd8508ed172df:0x91c69e01b7d171c3!2m2!1d11.4767234!2d48.1137459!1m5!1m1!1s0x479dd84e42969ae7:0x40d83d73aebe717c!2m2!1d11.4691102!2d48.1132028!3e2 | Google maps]] 
 +  * If the weather is bad you can take the 268 bus from the Großhadern subway stop to the Zinkgrafstraße or Waldhüterstraße and then walk through the pharmacy and chemistry buildings to the ISD. 
 +  * I will meet you at the entrance to the ISD that is on the Feodor-Lynen-Straße. 
 ==== Location  ==== ==== Location  ====
   * Room C11, Fifth Floor, Leopoldstraße 44   * Room C11, Fifth Floor, Leopoldstraße 44
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-==== Organizing Lab ====+==== Organisers ====
  
-Arbeitsgruppe fuer funktionelle, strukturelle und molekulare Bildgebung\\ +  * Virginia L. Flanagin (virginia.flanagin@lmu.de) 
-Neurologie und DSGZ-LMU\\ +  * Monica Emch (monica.emch@tum.de) 
-Klinikum der Universität München – Großhadern\\ +  * Joshua Yudice (joshua.yudice@lrz.uni-muenchen.de)
-Feodor-Lynen-Straße 19 \\ +
-81377 München \\ +
-<neuroimaging@med.uni-muenchen.de>+
  
  
-===== Downloads =====+==== Course Material ====
  
-**[[coursews1819:slides_ws1819   | Slides from the course]]** (restricted access)\\+**[[ncpcourse1819:ncpMaterial_ws1819   | Course contents, lecture slides, etc.]]** (restricted access)\\
 \\ \\
  
-==== Suggested Reading ====+==== Online resources ====
  
-[[http://www.fil.ion.ucl.ac.uk/spm/doc/books/hbf2|Human Brain Function, 2nd Edition]] -- PDF drafts of book chapters +== MR basics and physics ==
  
-[[http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf|SPM12 manual]]+[[http://www.simplyphysics.com/MRIntro.html|Animated introduction to MRI]] -- MRI animations \\ 
 +[[http://www.revisemri.com/|ReviseMRI.com]] -- Additional material for studying MRI \\ 
 +[[http://www.cis.rit.edu/htbooks/mri|The basics of MRI]] -- A more detailed introduction to MRI\\ 
 +[[http://www.healthcare.siemens.de/magnetic-resonance-imaging/magnetom-world/publications/mr-basics | MR Basics from Siemens]]. The book //magnets, spins, and resonances// and is a basic but solid reference for MR physics and image creation.
  
-[[http://www.humanbrainmapping.org/COBIDASreport|COBIDAS Report]] (The part on preprocessing starts around pg. 53)+== Analysis techniques == 
 +[[http://www.fil.ion.ucl.ac.uk/spm/doc/books/hbf2|Human Brain Function, 2nd Edition]] -- PDF drafts of book chapters\\  
 +[[http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf|SPM12 manual]] -- Manual to SPM \\
  
-[[http://www.healthcare.siemens.de/magnetic-resonance-imaging/magnetom-world/publications/mr-basics|Some Publications on MR Basics]]. Find the book //magnets, spins, and resonances// and other publications by Siemens for download on this webpage.+== Reporting data == 
 +[[http://www.humanbrainmapping.org/COBIDASreport|COBIDAS Report]] -- Guidelines on how to write a paper that used fMRI\\
  
-[[http://www.youtube.com/watch?v=snO68aJTOpM|Neuroanatomy lecture from Pinky and the Brain]]+== For fun == 
 +[[http://www.youtube.com/watch?v=snO68aJTOpM|Neuroanatomy lecture from Pinky and the Brain]]\\
  
-==== MRI Tutorials ==== 
  
-[[http://www.revisemri.com/|ReviseMRI.com]] -- Study material on MRI 
  
-[[http://www.cis.rit.edu/htbooks/mri|The basics of MRI]] -- introduction to MRI by Joseph P. Hornak 
  
-[[http://www.simplyphysics.com/MRIntro.html|Animated introduction to MRI]] 
  
  
-==== Software packages ==== 
  
-[[http://www.fmrib.ox.ac.uk/fsl/|FSL]] -- a software package for functional neuroimaging +==== Software packages ====
- +
-[[http://www.fil.ion.ucl.ac.uk/spm/|SPM]] -- a software package for functional neuroimaging +
- +
-[[http://www.mccauslandcenter.sc.edu/crnl/tools|MRIcro/MRIcron]] -- a software tool for image viewing and conversion +
- +
-[[http://www.mathworks.de/products/matlab/ |Matlab]] -- Commercial, programming language and environment for data analysis and computation+
  
 +[[http://www.fil.ion.ucl.ac.uk/spm/|SPM]] -- a software package for functional neuroimaging\\
 +[[http://www.mccauslandcenter.sc.edu/crnl/tools|MRIcro/MRIcron]] -- a software tool for image viewing and conversion\\
 +[[http://www.fmrib.ox.ac.uk/fsl/|FSL]] -- an alternative software package for functional neuroimaging (unix based)\\
ncp/ncpcourse1819.1540217918.txt.gz · Last modified: by vflanagin