Error in timelockstatistics

Fri May 28 23:29:27 CEST 2010

Hi Allen,

Thank you very much for the input - I got the Image Processing Toolbox and
am now able to make use of the clustering function.  I do have remaining
questions about the cluster analysis.  I tried looking at the code but still
can't figure out what type of clustering approach (e.g., k-means, fuzzy
logic, etc) is being used and how to adjust its clustering sensitivity,
independent of the cluster thresholding alpha.  Any help would be much
appreciated!

I know it's a bit pretentious to refer to one's own papers, but this is a
case where the question forces me:

Maris & Oostenveld (2007). Journal of Neuroscience Methods.

Good luck,

Eric

dr. Eric Maris
Donders Institute for Brain, Cognition and Behavior

Center for Cognition and F.C. Donders Center for Cognitive Neuroimaging

Radboud University
P.O. Box 9104
6500 HE Nijmegen
The Netherlands
T:+31 24 3612651
Mobile: 06 39584581

F:+31 24 3616066
E: e. <mailto:e.maris at donders.ru.nl> maris at donders.ru.nl

From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Nathan Weisz
Sent: Thursday, May 13, 2010 1:22 AM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] Error in timelockstatistics

Dear Allen,

you need bwlabeln anyhow, no matter how you want to cluster (the function
can cluster in n-dimensions). so getting the Image Processing Toolbox may be
a good investment if you decide to use fieldtrip statistics in future.

an -untested- alternative may be to use the octave version of bwlabeln.
usually the code is very compatible to matlab, i.e. if it does not run
out-of-the-box it usually just needs a little tweaking. however it may be a
lot slower.

http://users.powernet.co.uk/kienzle/octave/matcompat/scripts/image/bwlabel.m

http://www.gnu.org/software/octave/index.html

good luck,

nathan

On 13.05.2010, at 00:44, Allen Ardestani wrote:

Hi everyone,

I am having some difficulty using the cluster-based permutations in both
time and frequency domains.  I have just 8 channels of discrete LFP
positions, so I thought it may be problematic to cluster them together in
space.  I therefore first tried clustering only in time (ERP) or
time-frequency (ERS/ERD) by using a single channel.  I used  [stat] =
ft_timelockstatistics(cfg, ave_spatial, ave_non_spatial) with the following
cfg:

method: 'montecarlo'

statistic: 'indepsamplesT'

correctm: 'cluster'

clusteralpha: 0.0500

clusterstatistic: 'maxsum'

tail: 0

clustertail: 0

alpha: 0.0250

numrandomization: 100

design: [1x267 double]

channel: 'F1'

minnbchan: 0

layout: 'layout.mat'

ivar: 1

I get the following error message:

??? Undefined function or method 'bwlabeln' for input arguments of type
'double'.

Error in ==> findcluster at 89

  [labelmat(spatdimlev, :, :), num] = bwlabeln(reshape(onoff(spatdimlev, :,
:), nfreq, ntime), 4);

Error in ==> clusterstat at 194

      posclusobs = findcluster(reshape(postailobs,
[cfg.dim,1]),channeighbstructmat,cfg.minnbchan);

Error in ==> statistics_montecarlo at 321

  [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource);

Error in ==> statistics_wrapper at 285

    [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource);

Error in ==> ft_timelockstatistics at 96

[stat, cfg] = statistics_wrapper(cfg, varargin{:});

I'm assuming that part of the problem is that I don't have the Image
Processing Toolbox, but is there a way to specify to not cluster across
channels?  I'm a new user, so any advice is much appreciated.

Thanks in advance!

____________________________________________________________________________
______

Allen Ardestani    Email: aardesta at ucla.edu

Phone: (310) 825-5528

Medical Scientist Training Program

David Geffen School of Medicine at UCLA

Semel Institute for Neuroscience and Human Behavior

760 Westwood Plaza

Los Angeles, CA 90095-1759

USA

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

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/

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

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/neuroimaging/fieldtrip.
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