Within-subject coherence statististics for virtual sources

Lorina Naci lorina_naci at YAHOO.CO.UK
Wed Nov 8 20:00:27 CET 2006


Dear Jan-Mathijs,

  Thank you for the detailed help in your previous message.

  >For the time being, I assume that you have your data imported into a fieldtrip-like >format, using besa2fieldtrip. I am not familiar with this function, but when I read the >help of besa2fieldtrip I guess that your besa file was a .tfc file. So probably your >data-object looks like what fieldtrip considers to be a frequency-structure, containing >a TFR for each ROI. I guess you have two data-objects for each subject.

  One clarification: yes, i do have two data-object (or .tfc files) for each subject, one for each condition, but there are two types of .tfc files that I could use: either the raw time-frequency data for each condition, or the statistically analysed time-frequency data for that condition. BESA saves both of these as .tfc files. At the moment I am using the raw TFR data.


  I tried to run the script as you suggested but it did not work. The error message I get is to do with
  [stat] = statistics_wrapper(cfg, varargin{:}). It just gives me an error message pointing to this line,saying: error using fieldtrip-20061003/private/statistics_wrapper, could not determine the type of input data.

  Also, the function 'cfg.numrandomization' requires a number, but I am not sure what the choice of the number depends on? I've inputed 500 as in the documentation example.

  Finally, at risk making my ignorance of how Fieldtrip works entirely transparent, I am not quite sure how the function you send me 'statfun_diff.m' links with the 'freqstatistics.m,' and whether I do need to use it?

  I would greatly appreciate any help with this,

  Many thanks,
  Lorina






Jan Mathijs Schoffelen <Jan.Schoffelen at FCDONDERS.RU.NL> wrote:
        v\:* {behavior:url(#default#VML);}  o\:* {behavior:url(#default#VML);}  w\:* {behavior:url(#default#VML);}  .shape {behavior:url(#default#VML);}        st1\:*{behavior:url(#default#ieooui) }                Dear Lorina,

  For the time being, I assume that you have your data imported into a fieldtrip-like format, using besa2fieldtrip. I am not familiar with this function, but when I read the help of besa2fieldtrip I guess that your besa file was a .tfc file. So probably your data-object looks like what fieldtrip considers to be a frequency-structure, containing a TFR for each ROI. I guess you have two data-objects for each subject.
  What you would like to do is possible within fieldtrip, but I would advise you not to use clusterrandanalysis to get there. Quite some correspondence has been devoted to the new statistical interface, you can read about it on the discussion list’s website (follow the appropriate links on the fieldtrip website), concerning Re: clusterrandanalysis on scalar values + problem with topoplotER during the past month, but which started in August.
  In a nutshell: instead of using clusterrandanalysis you could use freqstatistics (under the above assumption that your data resembles a fieldtrip-frequency structure) with the appropriate settings to get your statistics done. Freqstatistics relies on statistics_montecarlo, when you specify cfg.method = ‘montecarlo’.
  Please have a try following the thread on the discussion list, and the following configuration settings, as well as the information in statistics_montecarlo and other dependent functions. You’ll probably need the attached function as well, which computes your statistic of interest.

  Cfg = [];
  Cfg.method = ‘montecarlo’;
  Cfg.statistic = ‘diff’;
  Cfg.parameter = ‘cohspctrm’; %This is at least what I expect your data objects to contain!
  Cfg.numrandomization = a number;
  Cfg.design = [1 1 2 2 3 3 with all the numbers in between 14 14; 

                       1 2 1 2 1 2 with all the numbers in between 1 2]; %this specifies how the data has to be interpreted
  Cfg.ivar = 2; %row-index of independent variable, which is the condition in your case
  Cfg.uvar = 1; %row-index of the ‘unit’-variable, your unit of observation, which are your individual subjects.
     %the design-matrix will be shuffled, by swapping the 1 and 2’s in the ivar-row, while keeping the uvar-doublets together.
  Cfg.correctm = ‘yes’; %keep it at this for the time being, we have to develop a cunning strategy to incorporate something about the neighbourhood structure of your ROIs
    %as soon as you get your script running, you can try to incorporate fancy multiple-comparison correction strategies, such as clustering in time and frequency.

  Stat = freqstatistics(cfg, subj1cond1, subj1cond2, subj2cond1, subj2cond2 
.); %take care that this corresponds with how you specified your design.

  Subjxconx should then be the data-structure containing your TFRs in a field called cohspctrm.

  I hope this puts you on track,

  Yours,

  Jan-Mathijs


---------------------------------

  From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Lorina Naci
Sent: Monday, October 23, 2006 7:18 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: [FIELDTRIP] Within-subject coherence statististics for virtual sources


    Dear FIELDTRIP members,



    I have used BESA to perform source coherence

    calculations for a multiple-subject/multiple-condition experiment. I have 14 subjects, and 2 conditions for which I’d like to compare coherence values. I have calculated coherence values in the Time-Frequency domain for each person.



    Given that BESA cannot calculate statistics in a multiple-subject study, their support personnel directed me towards FieldTrip.



    I would like to use your existing script ‘clusterrandanalysis on TFRs of power that were computed with BESA,’ but I cannot relate this to my data as the coherence values have been calculated for ROI sources, (8 per hemisphere - 16 sources total), and not for electrodes (I had 128).



    Do you have any advice regarding how I may adopt the script to for source coherence as opposed to electrode coherence? How do I import the source locations?



    Many thanks is advance for your help,

    Lorina

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