clusterrandanalysis input format
Rodrigo F. Salazar
rsalazar at NERVANA.MONTANA.EDU
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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