Neuroimaging

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
{{logo_imaging_lab_nur_hirne.jpg|Neuroimaging Group}}

====== Practical course methods in functional imaging ======



==== Time and schedule ====

|Date and time: |January 13 through 24, 2025 |
|               |tba., times may vary depending on availability of rooms and equipment |
|Schedule:      |Block course, 10 days |
|Location:      |Room D00.027, Grosshadernerstr. 2, 82152 Martinsried (see Campus Martinsried website [[http://www.biologie.uni-muenchen.de/anfahrt/index.html]]) and the room finder: https://www.lmu.de/raumfinder/#/building/bw2970/map\\ |

==== Registration ==== 
Please register by email to <neuroimaging@med.uni-muenchen.de>.

==== Summary ====  
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) - primarily task-based fMRI, morphometry and structural imaging including diffusion tensor imaging, and data analysis with e.g. SPM12, CAT12. 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.

{{ ::ws202425_week1.png?900}}

{{ ::ws202425_week2.png?900 |}}


**Goal:** The goal of this practical course is to give students the tools, knowledge and hands-on experience needed to plan, conduct, and analyse predominantly task-based fMRI experiments.

**Course objectives:** At the end of the course the students should be able to:
  * Critically evaluate the methodological quality of scientific work involving task-based fMRI
  * Work safely in an MRI environment 
  * Describe in their own words the relevant parameters of an fMRI data acquisition
  * List the necessary steps to prepare (f)MRI data for scientific analysis
  * Describe the limitations in interpreting fMRI data based on the nature of the fMRI signal 
  * Correctly design an fMRI study 
  * Choose the appropriate analysis for neuro-scientific and psychological research questions of the student’s choosing
  * Perform a basic task-based fMRI analysis using the toolbox Statistical Parametric Mapping (SPM) (version 12) for Matlab
  * Defend their choice of procedure for incidental findings in fMRI

**Concept:** In the first week of the course, there will be theoretical lectures on the topics listed below. In addition, there will be guided tutorials on how to analyse fMRI and structural MRI data with SPM12. The tutorials are self-paced. In the second week, you will have to analyse a data set on your own (although we will be available if you have questions). You will be graded on a final report on this data set to be handed in by 18:00 on last day of the course. 

 

==== FAQ ====
If you wish to read more about attendance, ECTS credits and missed hours, afternoons, weeks, in our list of 
[[imagingcourse_faq | frequently asked questions]].


^An upload link for the final projects will be added to the [[coursews2425:slides_ws2425 | restricted access section]].^

==== Session titles ====

  * The session titles can be found in the time plan above

==== Locations  ====
  * Room D00.027, Grosshadernerstr. 2, 82152 Martinsried (see Campus Martinsried Website [[http://www.biologie.uni-muenchen.de/anfahrt/index.html]], and the Room Finder at the LMU: [[https://www.lmu.de/raumfinder/#/building/bw2970/map]])
  * MRI Scanners, Campus Grosshadern, Marchioninistr. 15, 81377 München

==== List of speakers  ====

  * Dr. Rainer Bögle, Neurology
  * Prof. Dr. Olaf Dietrich, Clinical Radiology
  * Prof. Dr. Peter zu Eulenburg, DSGZ & Neuroradiology
  * Dr. Virginia Flanagin, DSGZ
  * Dr. Thomas Stephan, Neurology
  * PD Dr. Christian Vollmar, Neurology


==== Organizing Lab ====

Arbeitsgruppe fuer funktionelle, strukturelle und molekulare Bildgebung\\
Neurologie und DSGZ-LMU\\
Klinikum der Universität München – Großhadern\\
Fraunhoferstr. 20\\
82152 Planegg/Martinsried\\
<neuroimaging@med.uni-muenchen.de>


===== Downloads =====

**[[coursews2425:slides_ws2425   | Restricted access - slides and project information]]** 


==== Suggested Reading ====

  * [[http://www.fil.ion.ucl.ac.uk/spm/doc/books/hbf2|Human Brain Function, 2nd Edition]] -- PDF drafts of book chapters 
  * [[https://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf|SPM12 manual]], and [[https://www.fil.ion.ucl.ac.uk/spm/doc/|SPM documentation]], especially the [[https://www.fil.ion.ucl.ac.uk/spm/docs/|SPM tutorials]]
  * [[http://www.humanbrainmapping.org/COBIDASreport|COBIDAS Report]] (The part on preprocessing starts around pg. 53)
  * [[https://www.magnetomworld.siemens-healthineers.com/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.
  * [[https://fmrif.nimh.nih.gov/index.php/SummerCourse|NIH Summer School on Neuroimaging]] Lectures slides on various aspects of MRI data collection and analysis 
  * [[http://www.youtube.com/watch?v=snO68aJTOpM|Neuroanatomy lecture from Pinky and the Brain]]

 
==== MRI Tutorials ====

  * [[http://www.cis.rit.edu/htbooks/mri|The basics of MRI]] -- introduction to MRI by Joseph P. Hornak


==== Useful links =====
  * https://www.imaios.com/en/e-anatomy/brain/mri-axial-brain - an interactive tool to look at brain areas
  * https://www.neuroanatomy.ca/ - also a good set of tools for neuroanatomy


==== Software packages ====

  * [[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
  * [[https://neuro-jena.github.io/cat12-help/|CAT12 Toolbox]] -- a computational neuroanatomy toolbox for SPM12
  * [[https://www.nitrc.org/projects/mricron|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