clusterrandanalysis input format

Sun Sep 23 16:31:20 CEST 2007

Dear Rodrigo Salazar and Sameer Walawalkar,

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

1.	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.
2.	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.
3.	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 : <http://www.ru.nl/master/cns/>
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. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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