[FieldTrip] ft_freqstatistics in a 2 way ANOVA - design and implementation

[Justin Tanner]

I have a dataset consisting of 6 stimulation locations and 8 stimulation
intensities. I am trying to calculate a 2 way (6 by 8) anova with regards
to those two variables.

Each input structure consists of freq_loc#{intensity#} output of
ft_freqanalysis with just the chosen 10 trials of the respective conditions
(so for location1 and intensity 1, chosen trial indices are indicated in
cfg.trials).

   -  cfg.keeptrials = 'yes'


cfg.design = [loc ; int ; tri]

1 1 ... 1 1   ... 1 1 ... 1 1   ... 2 2 ... 2 2   ... 2 2 ... 2 2 ... 6 6
> ... 6 6
>
1 1 ... 1 1   ... 8 8 ... 8 8   ... 1 1 ... 1 1   ... 8 8 ... 8 8 ... 8 8
> ... 8 8
>
1 2 ... 9 10 ... 1 2 ... 9 10 ... 1 2 ... 9 10 ... 1 2 ... 9 10 ...1 2 ...
> 9 10
>

*OR*

   -  cfg.keeptrials = 'no'


cfg.design = [loc ; int]

1 1 ... 1 1   ... 1 1 ... 1 1   ... 2 2 ... 2 2   ... 2 2 ... 2 2 ... 6 6
> ... 6 6
>
1 1 ... 1 1   ... 8 8 ... 8 8   ... 1 1 ... 1 1   ... 8 8 ... 8 8 ... 8 8
> ... 8 8



For ft_freqstatistics:

cfg.method = 'montecarlo';
>
cfg.numrandomization = 500;

cfg.correctm = 'bonferroni' % Going to do 'cluster' once I define my
> distance function for neighbors
> cfg.alpha       = 0.05;
> cfg.tail        = 0;
> cfg.design=design;
> cfg.statistic='indepsamplesF';
> cfg.correcttail = 'prob';
>
> % Run with LOCATION as independent variable

> cfg.ivar=[1];
> [stat_loc] = ft_freqstatistics(cfg, freq_loc0{:}, freq_loc1{:},
> freq_loc2{:}, freq_loc3{:}, freq_loc4{:}, freq_loc5{:});


% Run with INTENSITY as independent variable

>  cfg.ivar=[2];

[stat_int] = ft_freqstatistics(cfg, freq_loc0{:}, freq_loc1{:},
> freq_loc2{:}, freq_loc3{:}, freq_loc4{:}, freq_loc5{:});
>


I want to ensure I am calling this appropriately. If I run it once with
cfg.ivar =1 and again with cfg.ivar = 2, is that calculating the main
effect of the cfg.design row's variable? First row is location, so running
cfg.ivar=1 is giving me a [num_chan X TFR ] stat.stat/prob/mask for
location, correct?

I feel that I am missing something that would allow for both comparisons in
one call of the ft_freqstatistics function, either in cfg properties or in
the cfg.design structuring / ft_freqanalysis output structuring.
Any clarification would be greatly appreciated.

-- 
Justin C. Tanner
Sensory Motor Research Group
Arizona State University
(360) 607-7544
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