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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. 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.
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 * Run DataDiagnostics - this is done by most [:aa:AutomaticAnalysisIntroduction] recipes if you choose to use this path  * Run DataDiagnostics - this is done by most [[aa|AutomaticAnalysisIntroduction]] recipes if you choose to use this path
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 * [:SliceTiming:Slice timing] - correcting for the fact that different slices in the brain are acquired at different times
 * [:FmBackground:Undistort EPIs using field maps] - usually no longer necessary on data from the Siemens scanner
 * [:MotionCorrection:Motion correction] - correcting for subject movement through an fMRI scan, sometimes called realignment
 * [[SliceTiming|Slice timing]] - correcting for the fact that different slices in the brain are acquired at different times
 * [[FmBackground|Undistort EPIs using field maps]] - usually no longer necessary on data from the Siemens scanner
 * [[MotionCorrection|Motion correction]] - correcting for subject movement through an fMRI scan, sometimes called realignment
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 * [:BasicOnsetFiles:Basic steps to making onset files]  * [[BasicOnsetFiles|Basic steps to making onset files]]
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 * [:MultiVoxelPatternAnalysis:Multi voxel pattern analysis (MVPA)]  * [[MultiVoxelPatternAnalysis|Multi voxel pattern analysis (MVPA)]]
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 * Introduction to fMRI methods: [:Introduction_to_fMRI_2010:(2010)] [:Introduction_to_fMRI_2011:(2011)]  * Introduction to fMRI methods: [[Introduction_to_fMRI_2010|(2010)]] [[Introduction_to_fMRI_2011|(2011)]]
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 * [http://www.fil.ion.ucl.ac.uk/spm/ FIL/SPM home page]  * [[http://www.fil.ion.ucl.ac.uk/spm/|FIL/SPM home page]]
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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.
 * [http://www.fil.ion.ucl.ac.uk/spm/dox.html Papers published by the FIL group on SPM] - these are available online via the SPM website, as are some other important papers on related theory.
 * [http://www.fil.ion.ucl.ac.uk/spm/course/ SPM course notes]
 * 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.
 * [[http://www.fil.ion.ucl.ac.uk/spm/dox.html|Papers published by the FIL group on SPM]] - these are available online via the SPM website, as are some other important papers on related theory.
 * [[http://www.fil.ion.ucl.ac.uk/spm/course/|SPM course notes]]
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 * ["Templates"]  * [[Templates]]
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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 [: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].
 * 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 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

Written guides

More advanced issues

Useful background

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