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• Define your design structure: FileStruct

    This argument is **required**. This is  the name of the a<sub>1</sub>by­a<sub>2</sub>by­...a<sub>m</sub> cell array that contains the names of the files to be analysed  (this will be your main job !)

Write down your*MyStructure* variable as below: (Suppose you have only .lena files and 3-way design of 2x3x2)
<file>
MyStructure{1,1,1}= {'file1111.lena', 'file1112.lena', .... 'file111n.lena'};
MyStructure{1,1,2}= {'file1121.lena', 'file1122.lena', .... 'file112n.lena'};
MyStructure{1,2,1}= {'file1211.lena', 'file1212.lena', .... 'file121n.lena'};

      .
     .
     .

MyStructures{2,3,2}= {'file2321.lena', 'file2322.lena', .... 'file232n.lena'};
</file>

• Write a script Script in matlab to provide information about your data as well as your experimental design:

Required arguments

• FactorLevelFactorlevel

This argument is required. It is an array of _m_ integers: \[a_1_, a_2_ ..a_m_] where _m_ is the number of factors and each a_i_ is the number of levels of the _ith_ factor\\
example:
<file>
mega_anova (...,'FactorLevel', \[3 2], ....) </file>
means that your design is made of two factors that have _3_ and _2_ levels respectively. Beware that the order in which you declare your factors is important and must be consistent throughout your parameters and variables definition.

• FileStruct

This argument is required.It is the variable MyStructure that you decalred above

example:
<file> mega_anova ('FactorLevel', \[3 2], 'FileStruct', MyStructure....)</file>

Optional arguments

• PathInPathin

This argument is optional. It is a string that specifies the Path to the folder where the input files (as defined in your FileStruct ) are located.If not specified, the files are searched in the current folder (displayed in Matlab)
Usage: <file> mega_anova (..., .....,.....,'PathIn', '/lena13/home_users/users/datalinks/MYMANIP') </file>
or
<file> mega_anova(.....,.....,'PathIn','/lena13/home_users/users/datalinks/MYMANIP/') </file>
The last slash is to be added if it is not specified in your FileStruct.

• PathOutPathout

This argument is optional. It is a string that specifies the path to the folder where to write the output .lena files of the analysis.If not specified, the files are written in the current folder.
Usage:
<file> mega_anova('PathOut','/pclxserver/data/users/datalinks/MYMANIP/MyAnovaResult') </file>
Note that you may or may not add a final slash to the folder specified, the program will deal with it.

• FilePrefixFileprefix

This argument is optional. It is a string that specifies the prefix of the output file. If not specified, the following default names are used:
FanovaEffect(i).lena
panovaEffect(i).lena
FanovaEffect(ij).lena
panovaEffect(ij).lena
i for the i ||th|| factor and (ij) for the interaction between the i||th|| and the j||th|| factors.
Usage: <file> mega_anova (..., 'FilePrefix', 'Pouet',...)</file> will produce the following output files if your design is made of two factors:
PouetF1.lena, Pouetp1.lena,
PouetF2.lena, Pouetp2.lena,
PouetF12.lena, Pouetp12.lena

• SignedF

This argument is optional. It is a small trick for advanced users. It is a Boolean used only in the case where each factor Ai has exactly two levels, with means mi1 and mi2 for the levels 1 and 2 of the ith factor.
If m_i1_<m_i2_, the F value for the effect of Ai will be multiplied by -1.
Note: This argument is a boolean and is single (is not a named argument with a name and a value)
Usage: <file> mega_anova (..., 'FilePrefix', 'Pouet','SignedF')</file>

...

This argument is optional. It is a boolean used only in case where -Log(p)is preferred to p value
Note: This argument is a boolean and is single (is not a named argument with a name and a value)
Usage: <file> mega_anova (..., 'FilePrefix', 'Pouet','SignedF', 'minusLogp')</file>

• design

This argument is optional but very important! It tells whether the design is*between_trials*, *between_subjects* or *within_subjects* (repeated measurments)\\
By default, the design is within-subject \\
Usage: <file> mega_anova ('FileStruct', MyStructure,...,'FactorLevel', \[3 2], 'FilePrefix', 'Pouet','SignedF', 'minusLogp', 'design', 'between_trials')</file>
<file> mega_anova ('FileStruct', MyStructure,...,'FactorLevel', \[3 2], 'FilePrefix', 'Pouet','SignedF', 'minusLogp', 'design', 'between_subjects')</file>

Very important!
If your design is between trials, you need to put only one file ( which includes all the trials) per condtion in your FileStruct variable

• format

This argument is also optional ! It is used to specify the format when it is *.mat*. By default, the format is *.lena/.ds/.fiff* \\
Usage: <file> mega_anova ('FileStruct', MyStructure,...,'FactorLevel', \[3 2], 'FilePrefix', 'Pouet','SignedF', 'minusLogp', 'design', 'between_trials', 'format', '.mat')</file>

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