[FieldTrip] Cluster Permutation Data Formatting

[Tavabi, Kambiz]

I am sorry but I don't understand this response from Doug.

-----Original Message-----
From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Douglas Rose
Sent: Monday, December 13, 2010 3:30 PM
To: nathanweisz at me.com
Cc: fieldtrip at donders.ru.nl
Subject: Re: [FieldTrip] Cluster Permutation Data Formatting

Sounds good.

I thought about it later and thought the shorter might not be too broad for someone not in the field.

Doug

>>> "Tavabi, Kambiz" <TAVABIK at email.chop.edu> 12/13/2010 2:42 PM >>>
Embarassing, off course I do! I apologize about that. However I am still having other downstream errors due to some of the definitions.  FYI I changed cfg.channel to {['MLT']; ['MRT']}. Running the script resulted in 

??? Undefined function or variable "sens".
Error in ==> ft_neighbourselection at 95
if ~isstruct(sens)
Error in ==> neighbourselection at 17
[varargout{1:nargout}] = funhandle(varargin{:});
Error in ==> statistics_wrapper at 241
    cfg.neighbours = neighbourselection(cfg,varargin{1});
Error in ==> ft_freqstatistics at 125
[stat, cfg] = statistics_wrapper(cfg, varargin{:});

I maybe misunderstanding what is clustered. Is it sensors or adjacent time-frequency bins? Because I only have two channels clustering adjacent sensors will fail. Perhaps you could advise on whether cfg.correctm ='cluster'; is the right choice. Should I consider another option? and if so what happens to:
cfg.clusteralpha     = 0.05;
cfg.clusterstatistic = 'maxsum';
cfg.minnbchan        = 2;
cfg.clustertail      = 0;

Is there another tutorial which discusses other routines for the various multiple comparison correction routines?
-K.
-------------------------------------------------------------
Kambiz Tavabi PhD
Biomedical Imaging Laboratory
The Children's Hospital of Philadelphia
34th Street and Civic Center Boulevard
Philadelphia, Pa. 19104
Tel: 267.426.0302
email: tavabik at email.chop.edu 
-------------------------------------------------------------
________________________________________
From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Nathan Weisz [nathanweisz at mac.com] 
Sent: Monday, December 13, 2010 2:12 PM
To: Email discussion list for the FieldTrip project
Subject: Re: [FieldTrip] Cluster Permutation Data Formatting

hi,

looks like you have a typo in your data structure (lable instead of label).

good luck,
n

On 13.12.2010, at 17:33, Tavabi, Kambiz wrote:

> Greetings, I am using the recommendations on http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock#within-subjects_experiments to carry out within-subjects permutation tests on MEG data from 10 subjects in a 2x2 design. Briefly, for each subject I have the conditional source-space (2 virtual electrodes) time-frequency representations computed between 1.5-80Hz (0.5 freq step) using Morlet wavelets throughout the stimulus duration (i.e., trial epochs from -0.8 - 1.6 sec). As per tutorial I have created data structures, which to the best of my knowledge are suitable for use with ft_freqstatistics(cfg, cond1, cond2). Also, I have minimally modified the routine in the tutorial to create the cfg structure. As the final state of the dataset was not arrived at using the FT pipeline I am afraid there might be input structure field(s) I may have not defined, or defined incorrectly (e.g. channel labling and layout). Essentially I simply wish to run the tests and view results on two time-frequency representation plots (eg., imagesc)! I would very much appreciate if someone with more experience in these routines would take a look at my script (see attachment) and e.g. data structure and let me know what is missing and/or wrong with them.
>
> ExpHi =
>         freq: [1x158 double]
>         time: [1x2880 double]
>    powspctrm: [4-D double]
>       dimord: 'subj_chan_freq_time'
>        lable: {2x1 cell} (ie., {['MLT']; ['MRT']}
>
> size(ExpHi.powspctrm) =
>          10           2         158        2880 (i.e., Subjects x channes x freqs x timepoints)
>
> Currently I am recieving the following errors
>
> ??? Reference to non-existent field 'label'.
> Error in ==> prepare_timefreq_data>forcedimord at 509
>  output.label  = input.label;
> Error in ==> prepare_timefreq_data at 87
>  [remember{c}, hascrsspctrm] = forcedimord(varargin{c}); Error in ==> statistics_wrapper at 217
>  [cfg, data] = prepare_timefreq_data(cfg, varargin{:}); Error in ==> ft_timelockstatistics at 117 [stat, cfg] = statistics_wrapper(cfg, varargin{:});
>
>
> -K.
> ------------------------------------------------------------
> Kambiz Tavabi PhD
> Biomedical Imaging Laboratory
> The Children's Hospital of Philadelphia
> 34th Street and Civic Center Boulevard
> Philadelphia, Pa. 19104
> Tel: 267.426.0302
> email: tavabik at email.chop.edu 
> ------------------------------------------------------------
>
> <ft_freqstats_script.m>_______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl 
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip 


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