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--- coursews2425 [2024/11/13 11:52] – vflanagin
+++ coursews2425 [2025/02/07 14:44] (current) – [Summary] vflanagin
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 ==== 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), morphometry and structural imaging including diffusion tensor imaging, simultaneous electroencephalography (EEG), 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.
+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_week1.png?900}}
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+**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 ====
@@ Line 66: / Line 83: @@
   * [[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]]
-  * [[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]]
   * [[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]]
@@ Line 78: / Line 92: @@
 ==== MRI Tutorials ====
-[[http://www.cis.rit.edu/htbooks/mri|The basics of MRI]] -- introduction to MRI by Joseph P. Hornak
+  * [[http://www.cis.rit.edu/htbooks/mri|The basics of MRI]] -- introduction to MRI by Joseph P. Hornak
@@ Line 88: / Line 102: @@
 ==== Software packages ====
-[[http://www.fmrib.ox.ac.uk/fsl/|FSL]] -- a software package for functional neuroimaging
+  * [[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.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
-[[https://neuro-jena.github.io/cat12-help/|CAT12 Toolbox]] -- a computational neuroanatomy toolbox for SPM12
+  * [[http://www.mathworks.de/products/matlab/ |Matlab]] -- Commercial, programming language and environment for data analysis and computation
-[[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