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--- ncp:ncpcourse1819 [2018/10/22 14:11] – [Time and schedule] vflanagin
+++ ncp:ncpcourse1819 [2018/11/10 12:08] (current) – [Visit to the MRI machine] vflanagin
@@ Line 5: / Line 5: @@
 ==== 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)
@@ Line 18: / Line 18: @@
-==== 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.
-==== Session titles ====
+In the last part of the course, you will also have tutorials, these will be longer than the lecture part of the course.
-  * Please find the session titles in the Time Plan (coming soon)
-==== Locations  ====
-  * Room D00.0027, [[http://www.uni-muenchen.de/funktionen/gebaeudeplaene/2971_d_00.pdf|D00.0027 Biozentrum]], Grosshadernerstr. 2, 82152 Martinsried (see Campus Martinsried Website [[http://www.biologie.uni-muenchen.de/anfahrt/index.html|here]])
-  * MRI Scanners, Neuroradiology and Radiology, Klinikum Grosshadern, Marchioninistr. 15, 81377 München
-==== List of speakers  ====
-  * Dr. Rainer Bögle, Neurology
+== Learning Objectives ==
-  * PD Dr. Guido Böning, Nuclear Medicine
+At the end of this course, students should be able to:
-  * PD Dr. Olaf Dietrich, Clinical Radiology
-  * Dr. Matthias Ertl, Neurology
-  * Prof. Dr. Peter zu Eulenburg, Neuroradiology
-  * Dr. Virginia Flanagin, IFB
-  * Dr. Victor Spoormaker, MPI Psychiatry
-  * Dr. Thomas Stephan, Neurology
-  * PD Dr. Christian Vollmar, Neurology
-  * Dipl.-Biol. Mathias Hübner, ISD
+  * 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 ====
-==== Organizing Lab ====
+  * Slot 1: 16.11.2018 at 12:00 - 13:30
+  * Slot 2: 16.11.2018 at 15:30 - 17:00
-Arbeitsgruppe fuer funktionelle, strukturelle und molekulare Bildgebung\\
-Neurologie und DSGZ-LMU\\
-Klinikum der Universität München – Großhadern\\
-Feodor-Lynen-Straße 19 \\
-München \\
-<neuroimaging@med.uni-muenchen.de>
+== 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
-===== Downloads =====
-**[[coursews1819:slides_ws1819   | Slides from the course]]** (restricted access)\\
-\\
-==== Suggested Reading ====
-[[http://www.fil.ion.ucl.ac.uk/spm/doc/books/hbf2|Human Brain Function, 2nd Edition]] -- PDF drafts of book chapters
+==== Organisers ====
-[[http://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf|SPM12 manual]]
+  * Virginia L. Flanagin (virginia.flanagin@lmu.de)
+  * Monica Emch (monica.emch@tum.de)
+  * Joshua Yudice (joshua.yudice@lrz.uni-muenchen.de)
-[[http://www.humanbrainmapping.org/COBIDASreport|COBIDAS Report]] (The part on preprocessing starts around pg. 53)
-[[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.
+==== Course Material ====
-[[http://www.youtube.com/watch?v=snO68aJTOpM|Neuroanatomy lecture from Pinky and the Brain]]
+**[[ncpcourse1819:ncpMaterial_ws1819   | Course contents, lecture slides, etc.]]** (restricted access)\\
+\\
-==== MRI Tutorials ====
+==== Online resources ====
-[[http://www.revisemri.com/|ReviseMRI.com]] -- Study material on MRI
+== MR basics and physics ==
-[[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]] -- 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.simplyphysics.com/MRIntro.html|Animated introduction to MRI]]
+== 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\\
-==== Software packages ====
+== For fun ==
+[[http://www.youtube.com/watch?v=snO68aJTOpM|Neuroanatomy lecture from Pinky and the Brain]]\\
-[[http://www.fmrib.ox.ac.uk/fsl/|FSL]] -- a software package for functional neuroimaging
-[[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
+==== 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)\\