Neuroimaging

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====== NCP Course N: fMRI / WS201819 ======



==== Time and schedule ====

|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 2: Experimental Design (Monica Emch)
  * Part 3: fMRI data analysis (Virginia Flanagin
  * Part 4: Tutorial for data analysis (Joshua Yudice)







==== Summary & Objectives ====  
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 ====

  * 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  ====
  * Room C11, Fifth Floor, Leopoldstraße 44



 

==== Organisers ====

  * Virginia L. Flanagin (virginia.flanagin@lmu.de)
  * Monica Emch (monica.emch@tum.de)
  * Joshua Yudice (joshua.yudice@lrz.uni-muenchen.de)


==== Course Material ====

**[[ncpcourse1819:ncpMaterial_ws1819   | Course contents, lecture slides, etc.]]** (restricted access)\\
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==== Online resources ====

== MR basics and physics ==

[[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.

== 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 \\

== Reporting data ==
[[http://www.humanbrainmapping.org/COBIDASreport|COBIDAS Report]] -- Guidelines on how to write a paper that used fMRI\\

== For fun ==
[[http://www.youtube.com/watch?v=snO68aJTOpM|Neuroanatomy lecture from Pinky and the Brain]]\\







==== 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.fmrib.ox.ac.uk/fsl/|FSL]] -- an alternative software package for functional neuroimaging (unix based)\\