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reference:ft_analysispipeline [2018/08/23 14:43] (current)
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 +=====  FT_ANALYSISPIPELINE =====
 +
 +Note that this reference documentation is identical to the help that is displayed in MATLAB when you type "help ft_analysispipeline"​.
 +
 +<​html><​pre>​
 +  FT_ANALYSIPIPELINE reconstructs the complete analysis pipeline that was used to create
 +  the input FieldTrip data structure. The pipeline will be visualized as a flowchart.
 +  In the future it will be possible to output the complete pipeline as a MATLAB script
 +  or in a specialized pipeline format (e.g. PSOM, JIST, LONI, Taverna).
 + 
 +  Use as
 +    output = ft_analysispipeline(cfg,​ data)
 + 
 +  The first cfg input contains the settings that apply to the behaviour of this
 +  particular function and the second data input argument can be the output of any
 +  FieldTrip function, e.g. <a href=/​reference/​ft_preprocessing><​font color=green>​FT_PREPROCESSING</​font></​a>,​ <a href=/​reference/​ft_timelockanalysis><​font color=green>​FT_TIMELOCKANALYSIS</​font></​a>,​ <a href=/​reference/​ft_sourceanalysis><​font color=green>​FT_SOURCEANALYSIS</​font></​a>,​
 +  <a href=/​reference/​ft_freqstatistics><​font color=green>​FT_FREQSTATISTICS</​font></​a>​ or whatever you like.
 + 
 +  Alternatively,​ for the second input argument you can also only give the configuration
 +  of the processed data (i.e. "​data.cfg"​) instead of the full data.
 + 
 +  The configuration options that apply to the behaviour of this function are
 +    cfg.filename ​  = string, filename without the extension
 +    cfg.filetype ​  = string, can be '​matlab',​ '​html'​ or '​dot'​
 +    cfg.feedback ​  = string, '​no',​ '​text',​ '​gui'​ or '​yes',​ whether text and/or
 +                     ​graphical feedback should be presented (default = '​yes'​)
 +    cfg.showinfo ​  = string or cell array of strings, information to display
 +                     in the gui boxes, can be any combination of
 +                     '​functionname',​ '​revision',​ '​matlabversion',​
 +                     '​computername',​ '​username',​ '​calltime',​ '​timeused',​
 +                     '​memused',​ '​workingdir',​ '​scriptpath'​ (default =
 +                     '​functionname',​ only display function name). Can also
 +                     be '​all',​ show all pipeline. Please note that if you want
 +                     to show a lot of information,​ this will require a lot
 +                     of screen real estate.
 +    cfg.remove ​    = cell-array with strings, determines which objects will
 +                     be removed from the configuration prior to writing it to
 +                     file. For readibility of the script, you may want to
 +                     ​remove the large objectssuch as event structure, trial
 +                     ​definition,​ source positions
 +   ​cfg.keepremoved = '​yes'​ or '​no',​ determines whether removed fields are
 +                     ​completely removed, or only replaced by a short textual
 +                     ​description (default = '​no'​)
 + 
 +  This function uses the nested cfg and cfg.previous that are present in
 +  the data structure. It will use the configuration and the nested previous
 +  configurations to climb all the way back into the tree. This funtction
 +  will print a complete MATLAB script to screen (and optionally to file).
 +  Furthermore,​ it will show an interactive graphical flowchart
 +  representation of the steps taken during the pipeline(i). In the flowchart
 +  you can click on one of the steps to see the configuration details of
 +  that pipeline(i).
 + 
 +  Note that the nested cfg and cfg.previous in your data might not contain
 +  all details that are required to reconstruct a complete and valid
 +  analysis script.
 + 
 +  To facilitate data-handling and distributed computing you can use
 +    cfg.inputfile ​  ​= ​ ...
 +  If you specify this, the input data will be read from a *.mat file on disk. The
 +  file should contain only a single variable, corresponding with the input structure.
 + 
 +  See also <a href=/​reference/​ft_preprocessing><​font color=green>​FT_PREPROCESSING</​font></​a>,​ <a href=/​reference/​ft_timelockanalysis><​font color=green>​FT_TIMELOCKANALYSIS</​font></​a>,​ <a href=/​reference/​ft_freqanalysis><​font color=green>​FT_FREQANALYSIS</​font></​a>,​ <a href=/​reference/​ft_sourceanalysis><​font color=green>​FT_SOURCEANALYSIS</​font></​a>,​
 +  <a href=/​reference/​ft_connectivityanalysis><​font color=green>​FT_CONNECTIVITYANALYSIS</​font></​a>,​ <a href=/​reference/​ft_networkanalysis><​font color=green>​FT_NETWORKANALYSIS</​font></​a>​
 +</​pre></​html>​