clusterrandanalysis input format

Wed Sep 26 00:32:24 CEST 2007

Dear Eric and Sameer,

Thanks for correcting the bug and about the tutorial on  
clusterandanalysis.

I can now run freqanalysis_mtmfft but when I use the output to run  
clusterandanalysis, I have one error due to an empty 'stats'  
variable. I am now using the tutorial data to run clusterandanalysis  
to avoid problems due my data format. Even though I have noticed that  
in clusterrandstatistics.m,  the variables 'crspctrc1' and  
'crspctrc2' (line 678 and 679) are empty. I think that this is  
produced by a wrong input format.

I selected the two first channels of FICpreproc FCpreproc and instead  
of running timelockanalysis, I ran freqanalysis using

cfg =

  method: 'mtmfft'
        tapsmofrq: 4
          calcdof: 'yes'
       keeptapers: 'no'
       keeptrials: 'yes'
              pad: 0.5000
            taper: 'dpss'
           foilim: [0 100]
           output: 'powandcsd'
       channelcmb: {'MLC11'  'MLC12'}
          channel: {2x1 cell}

That gave me:

FICfreq =

         label: {2x1 cell}
        dimord: 'rpt_chan_freq'
          freq: [1x51 double]
     powspctrm: [85x2x51 double]
      labelcmb: {'MLC11'  'MLC12'}
     crsspctrm: [85x1x51 double]
     cumsumcnt: [85x1 double]
     cumtapcnt: [85x1 double]
           dof: [85x51 double]
          grad: [1x1 struct]
           cfg: [1x1 struct]

and

FCfreq =

         label: {2x1 cell}
        dimord: 'rpt_chan_freq'
          freq: [1x51 double]
     powspctrm: [84x2x51 double]
      labelcmb: {'MLC11'  'MLC12'}
     crsspctrm: [84x1x51 double]
     cumsumcnt: [84x1 double]
     cumtapcnt: [84x1 double]
           dof: [84x51 double]
          grad: [1x1 struct]
           cfg: [1x1 struct]

and then I ran clusterandanalysis using

cfg2 =

        statistic: 'indepsamplesZcoh'
             elec: [1x1 struct]
      chancmbgeom: 'free'
      alphathresh: 0.0500
            alpha: 0.0500
     makeclusters: 'no'

As following

[clusrand] = clusterrandanalysis(cfg2, FCfreq, FICfreq)

And if I use cfg2.makeclusters = 'yes', I get an empty 'clusrand'  
variable.

Do you have an idea where I am misusing the code?

Basically I simply would like to test the difference in coherence  
between the FIC and FC condition for the two first channels.

Thanks,

Rodrigo.

On Sep 23, 2007, at 8:31 AM, Eric Maris wrote:
Dear Rodrigo Salazar and Sameer Walawalkar,

You are both involved in similar analyses, and therefore I address  
you both.

There was a bug in the latest version of freqanalysis_mtmfft, which  
caused the error message in Rodrigo’s analysis. Sameer used an older  
version of freqanalysis_mtmfft, in which this bug was not yet  
present. I have corrected the bug and within a couple of days you can  
download the new m-file from the FT homepage.
There were a few bugs in the private function clusterrandstatistics.m  
related to the postprocessing of the results of a onesided  
statistical test. I have corrected these bugs. I now obtain identical  
p-values for the elements of posclusters in (1) a twosided analysis  
with cfg.alphathresh=0.05 and (2) a onesided analysis  
(cfg.onetwo=onesided_1<2) with cfg.alphathresh=0.025, as it should  
be. Similarly, I now obtain identical p-values for the elements of  
negclusters in (1) a twosided analysis with cfg.alphathresh=0.05 and  
(2) a onesided analysis (cfg.onetwo=onesided_2<1) with  
cfg.alphathresh=0.025, again as it should be.
Sameer has selected channel combinations by specifying cfg.channelcmb= 
{refchan ‘MEG’}. This only gives you the channel pairs in which your  
reference channel is in the first position. As a result, you will not  
select the channel pairs in which the reference channel is in the  
second position. I must admit that I was not aware of this problem. I  
advise you to use the labelcmb-field in the output of freqanalysis.  
 From this field, you can easily select those channel pairs in which  
the reference channel is in either the first or the second position,  
and pass this selection via the cfg.channelcmb-field.

Good luck,

Eric Maris

dr. Eric Maris

NICI/Biological Psychology and

F.C. Donders Center for Cognitive NeuroImaging

University of Nijmegen

P.O. Box 9104

6500 HE Nijmegen

The Netherlands

T:+31 24 3612651 (NICI)

T:+31 24 3610754 (FCDC)

F:+31 24 3616066 (NICI)

E: maris at nici.ru.nl

MSc Cognitive Neuroscience :www.ru.nl/master/cns/

From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On  
Behalf Of Rodrigo F. Salazar

Sent: Friday, September 21, 2007 7:16 PM

To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] clusterrandanalysis input format

Hi Eric,

Thanks for your quick reply. I scanned the tutorials and I could not  
find one that is using clusterrandanalysis.m. I only found a matlab  
script named:

"Apply clusterrandanalysis on TFRs of power that were computed with  
BESA"

but as it is only a script I cannot access the data.

So far I was capable to run freqanalysis.m by adapting my data to the  
format described in the documentation. However, when I run  
clusterranalaysis.m with the output of freqanalysis.m being 'freq'

[clusrand] = clusterrandanalysis(cfg2,freq,freq); % I am using twice  
'freq' as a test run with cfg2.statistic: 'indepsamplesZcoh'

, I keep on getting errors such as :

??? Reference to non-existent field 'dof'.

Error in ==> fieldtrip-lite-20070920/private/clusterrandstatistics at  
680

dofc1=reshape(sum(data.dof(replselc1,:,:),1),1,nfreq,ntime);

And if I had the option:

cfg.calcdof = 'yes'

to get the degree of freedom, I get this other error:

??? Undefined function or variable "cumtapcnt".

Error in ==> freqanalysis_mtmfft at 389

if calcdof && ~exist(cumtapcnt)

Could you please tell if I am using a wrong configuration variable or  
if there is a problem in the code?

Thanks,

Rodrigo.

On Sep 20, 2007, at 9:56 AM, Rodrigo F. Salazar wrote:

Hi,

I am new to fieldtrip and I am working with intracortical data. I  
have never used any function of fieldtrip and I would like to use  
clusterrandanalysis.m using my own data format. I cannot find a clear  
description of the input needed for that function. Can someone  
quickly describe the input format or even send me an example of input  
data?

Thanks,

Rodrigo.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Rodrigo F. Salazar, Ph.D

Post-doctoral Fellow

Lewis Hall 1,

Center for Computational Biology

Montana State University

Bozeman, 59717 MT, USA

Phone: ++1 (406) 994 71 90,

Fax: ++1 (406) 994 74 38

email: rsalazar at nervana.montana.edu

http://cns.montana.edu/~rsalazar/

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

The aim of this list is to facilitate the discussion between users of  
the FieldTrip toolbox, to share experiences and to discuss new ideas  
for MEG and EEG analysis.

http://listserv.surfnet.nl/archives/fieldtrip.html

http://www.ru.nl/fcdonders/fieldtrip/

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Rodrigo F. Salazar, Ph.D

Post-doctoral Fellow

Lewis Hall 1,

Center for Computational Biology

Montana State University

Bozeman, 59717 MT, USA

Phone: ++1 (406) 994 71 90,

Fax: ++1 (406) 994 74 38

email: rsalazar at nervana.montana.edu

http://cns.montana.edu/~rsalazar/

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

The aim of this list is to facilitate the discussion between users of  
the FieldTrip toolbox, to share experiences and to discuss new ideas  
for MEG and EEG analysis.

http://listserv.surfnet.nl/archives/fieldtrip.html

http://www.ru.nl/fcdonders/fieldtrip/

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

The aim of this list is to facilitate the discussion between users of  
the FieldTrip toolbox, to share experiences and to discuss new ideas  
for MEG and EEG analysis.

http://listserv.surfnet.nl/archives/fieldtrip.html

http://www.ru.nl/fcdonders/fieldtrip/

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Rodrigo F. Salazar, Ph.D
Post-doctoral Fellow
Lewis Hall 1,
Center for Computational Biology
Montana State University
Bozeman, 59717 MT, USA
Phone: ++1 (406) 994 71 90,
Fax: ++1 (406) 994 74 38
email: rsalazar at nervana.montana.edu
http://cns.montana.edu/~rsalazar/
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On Sep 20, 2007, at 9:56 AM, Rodrigo F. Salazar wrote:

> Hi,
>
> I am new to fieldtrip and I am working with intracortical data. I  
> have never used any function of fieldtrip and I would like to use  
> clusterrandanalysis.m using my own data format. I cannot find a  
> clear description of the input needed for that function. Can  
> someone quickly describe the input format or even send me an  
> example of input data?
>
> Thanks,
>
> Rodrigo.
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Rodrigo F. Salazar, Ph.D
> Post-doctoral Fellow
> Lewis Hall 1,
> Center for Computational Biology
> Montana State University
> Bozeman, 59717 MT, USA
> Phone: ++1 (406) 994 71 90,
> Fax: ++1 (406) 994 74 38
> email: rsalazar at nervana.montana.edu
> http://cns.montana.edu/~rsalazar/
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
>
>
>
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users  
> of the FieldTrip toolbox, to share experiences and to discuss new  
> ideas for MEG and EEG analysis.
>
> http://listserv.surfnet.nl/archives/fieldtrip.html
>
> http://www.ru.nl/fcdonders/fieldtrip/

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Rodrigo F. Salazar, Ph.D
Post-doctoral Fellow
Lewis Hall 1,
Center for Computational Biology
Montana State University
Bozeman, 59717 MT, USA
Phone: ++1 (406) 994 71 90,
Fax: ++1 (406) 994 74 38
email: rsalazar at nervana.montana.edu
http://cns.montana.edu/~rsalazar/
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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