Diff for "AnalysisPrinciples" - MRC CBU Imaging Wiki
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= Principles of analysis =
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Below is an outline list of the areas of theory involved in functional imaging, and related documents that may help. Unfortunately some of these sources are difficult, but in my experience, all of them repay a slow reread, even if you think you understood almost nothing first time round. There is a bias towards SPM, but the same principles usually apply to other imaging packages.  Below is an outline list of the areas of theory involved in functional imaging, and related documents that may help. Unfortunately some of these sources are difficult, but in my experience, all of them repay a slow reread, even if you think you understood almost nothing first time round. There is a bias towards SPM, but the same principles usually apply to other imaging packages.
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= General imaging introductions = = Introduction to imaging =
== Basic checks ==
 * Check for CommonArtefacts
 * Run DataDiagnostics - this is done by most [:aa:AutomaticAnalysisIntroduction] recipes if you choose to use this path
 * If you are unfortunate enough to find bad data, consider whether to RemoveBadScans
== Typical pre-processing stages ==
These are the stages typical to most analyses
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== Pre-processing ==
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 * [wiki:FmBackground Undistort EPIs using field maps] - usually no longer necessary on data from the Siemens scanner  * [:FmBackground:Undistort EPIs using field maps] - usually no longer necessary on data from the Siemens scanner
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 * [:BasicOnsetFiles:Basic steps to making onset files]
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 * [:MultiVoxelPatternAnalysis:Multi voxel pattern analysis (MVPA)]
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 * Rik Henson's SpmMiniCourse2008
  * Rik Henson's SpmMiniCourse
 * Introduction to fMRI methods: [:Introduction_to_fMRI_2010:(2010)] [:Introduction_to_fMRI_2011:(2011)]
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 * The [http://www.fil.ion.ucl.ac.uk/spm/doc/books/hbf2/ Human Brain Function book] - these are a series of chapters covering theory and to some extent implementation in SPM of the areas below. Be warned that some of these chapters are aimed at quite a high level, and may be hard to follow for those without relevant background.   * The [http://www.fil.ion.ucl.ac.uk/spm/doc/books/hbf2/ Human Brain Function book] - these are a series of chapters covering theory and to some extent implementation in SPM of the areas below. Be warned that some of these chapters are aimed at quite a high level, and may be hard to follow for those without relevant background.
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 * [wiki:Templates Templates]  * ["Templates"]
 * FmriAnalysisProblems
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 * A very basic [http://imaging.mrc-cbu.cam.ac.uk/pdfs/matrices.pdf primer on matrices], in pdf format (see the [wiki:ReadingOnlineDocs online reading page] if you need help with pdf documents).		  * ImagingJournals
 * A very basic [http://imaging.mrc-cbu.cam.ac.uk/pdfs/matrices.pdf primer on matrices], in pdf format (see the [:ReadingOnlineDocs:online reading page] if you need help with pdf documents).
 * This is a systematic and well-illustrated [http://www.ee.surrey.ac.uk/Teaching/Unix/ introduction to linux].
 * If you've never used shell scripting before, this [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/Primer_ShellScripting primer on shell scripting] or this [http://www.freeos.com/guides/lsst/ tutorial] would be a start.
 * For Matlab, you can look at [http://www.mathworks.com/academia/student_center/tutorials/launchpad.html tutorials and demos] offered by Mathworks itself. This site also contains links to Matlab tutorials at some universities. You may want to start with the [http://www.mathworks.com/access/helpdesk/help/pdf_doc/matlab/getstart.pdf Getting Started] section. The short introduction to [http://www.antoniahamilton.com/matlab_for_psychologists.pdf Matlab for psychologists] from the University of Nottingham is also useful.
 * The scripting language [http://www.python.org/ Python] is increasingly becoming popular for its flexibility and simplicity. You could start with the [http://wiki.python.org/moin/BeginnersGuide Beginners' Guide].
 * Look here for more information on [http://imaging.mrc-cbu.cam.ac.uk/imaging/AnalysisSoftware software].

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Principles of analysis

The aim of these pages is to introduce the theory behind different processing stages. If you're interested in the practicalities of how to do an analysis, you might want the [:AnalysisSoftware:software] page instead.

Below is an outline list of the areas of theory involved in functional imaging, and related documents that may help. Unfortunately some of these sources are difficult, but in my experience, all of them repay a slow reread, even if you think you understood almost nothing first time round. There is a bias towards SPM, but the same principles usually apply to other imaging packages.

Introduction to imaging

Basic checks

Typical pre-processing stages

These are the stages typical to most analyses

Statistics

Introductions to the theory and algorithms behind SPM

Presentations

  • CBU SpmMiniCourse2007

  • Rik Henson's SpmMiniCourse

  • Introduction to fMRI methods: [:Introduction_to_fMRI_2010:(2010)] [:Introduction_to_fMRI_2011:(2011)]

Written guides

More advanced issues

Useful background

CbuImaging: AnalysisPrinciples (last edited 2013-03-09 12:58:53 by RussellThompson)