Dear David, <br><br>I have had the same problem after end of August fieldtrip update. I had the right toolbox, but matlab couldn't find the path to it. I just added the exact path for randperm in setpath, which solved the problem.<br>
<br>Best, <br>Anna.<br><br><br><div class="gmail_quote">2011/9/13 <span dir="ltr"><<a href="mailto:fieldtrip-request@donders.ru.nl">fieldtrip-request@donders.ru.nl</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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Today's Topics:<br>
<br>
1. bufferviewer C++ code (JustinChen)<br>
2. ft_freqstatistics issue (??? Undefined function or method<br>
'randperm' for input arguments of type 'double'.) (Davide Rivolta)<br>
3. Re: ft_freqstatistics issue (??? Undefined function or method<br>
'randperm' for input arguments of type 'double'.)<br>
(Roemer van der Meij)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 12 Sep 2011 18:07:36 -0400<br>
From: JustinChen <<a href="mailto:justin.sickkids@hotmail.com">justin.sickkids@hotmail.com</a>><br>
To: <<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>><br>
Subject: [FieldTrip] bufferviewer C++ code<br>
Message-ID: <BAY152-W1973669968BE6CA059B9EFF9020@phx.gbl><br>
Content-Type: text/plain; charset="gb2312"<br>
<br>
<br>
<br>
<br>
<br>
Hey, all, Recently I want to try to compile the bufferviewer C++ source code under the directory: fieldtrip/realtime/utilities/viewer/. I tried to use the Microsoft Visual C++ IDE to compile the code but it failed, and now I am using the Eclipse+MinGW under the windows environment to compile it. Does anyone know what environment the C++ codes were compiled and debugged originally? And also I notice the code uses the FLTK API pakage to draw the GUI part, any other API libraries required to compile the code? Anybody who is familiar with the code please reply and I really appreciate your help. Thanks and have a good day! Justin<br>
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Message: 2<br>
Date: Tue, 13 Sep 2011 09:38:49 +0200<br>
From: Davide Rivolta <<a href="mailto:drivolta81@gmail.com">drivolta81@gmail.com</a>><br>
To: <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
Subject: [FieldTrip] ft_freqstatistics issue (??? Undefined function<br>
or method 'randperm' for input arguments of type 'double'.)<br>
Message-ID:<br>
<<a href="mailto:CAMkcSw7VcTOp6rHZhFCyWxWFTwZ6BJTbNH5wgbuhTDh6W9Mbkg@mail.gmail.com">CAMkcSw7VcTOp6rHZhFCyWxWFTwZ6BJTbNH5wgbuhTDh6W9Mbkg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear fieldtrippers,<br>
<br>
I wish to calculate the stat difference between stimulus and baseline in a<br>
group of subjects. I use ft_freqgrandaverage to average across subjects and<br>
then ft_freqstatistics (cluster statistic) to compare the 2 conditions<br>
(baseline & stimuli).<br>
<br>
I get this error: ??? Undefined function or method 'randperm' for input<br>
arguments of type 'double'.<br>
<br>
I tried even with the newest version (20110911) but the problem persists. I<br>
am not sure what I have to do.<br>
<br>
Any advice would be super. The script is below.<br>
<br>
Thanks a lot,<br>
<br>
Davide<br>
<br>
<br>
<br>
datainpath = '/data/home1/drivolta/Out4VG/DATA/';<br>
dataoutpath = '/data/home1/drivolta/Out4VG/DATA/';<br>
<br>
% Controls<br>
Controls = {<br>
'ASS31_TFR_high.mat';<br>
'CSA07_TFR_high.mat';<br>
'BMR08_TFR_high.mat';<br>
'NPD18_TFR_high.mat';<br>
%'BSA08_TFR_high.mat';<br>
%'ABE08_TFR_high.mat';<br>
%'EES05_TFR_high.mat';<br>
%'GPS10_TFR_high.mat';<br>
%'SDA01_TFR_high.mat';<br>
%'CSA17_TFR_high.mat';<br>
%'KBZ16_TFR_high.mat';<br>
<br>
};<br>
<br>
%--------------------------------------------------------------------------<br>
NControls = length(Controls);<br>
<br>
%% CONCATENATE DATA<br>
for i = 1:length(Controls)<br>
fullname = strcat(datainpath, Controls{i,1});<br>
load(fullname);<br>
<br>
% Activation time window<br>
TFR2 = power_continue_high; %Rename to change (select time window)<br>
idx = find((TFR2.time >= 0.5) &(TFR2.time <= 1.5));<br>
TFR2.powspctrm = power_continue_high.powspctrm(:, :,idx);<br>
TFR2.time = power_continue_high.time(idx);<br>
Stimuli{i} = TFR2;<br>
<br>
% Baseline time window<br>
TFR3 = power_continue_high;<br>
idx = find((TFR3.time >= -1) &(TFR3.time < 0));<br>
TFR3.powspctrm = power_continue_high.powspctrm(:,:, idx);<br>
TFR3.time = TFR2.time;<br>
Baseline{i} = TFR3;<br>
<br>
clear power_continue_high<br>
clear TFR2<br>
clear TFR3<br>
end;<br>
save Controls2Statistics Stimuli Baseline;<br>
<br>
<br>
<br>
cfg = [];<br>
cfg.channel = {'MEG', '-MRO31', '-MRO21'};<br>
cfg.keepindividual = 'yes';<br>
<br>
BaselineAll = ft_freqgrandaverage(cfg, Baseline{:});<br>
StimuliAll = ft_freqgrandaverage(cfg, Stimuli{:});<br>
<br>
<br>
<br>
load /data/home1/drivolta/Out4VG/DATA/GRAD % File with a structure<br>
containing grad field<br>
<br>
cfg = [];<br>
cfg.method = 'triangulation';<br>
cfg.neighbourdist = 5;<br>
cfg.grad = TFR.grad;<br>
cfg.layout = 'CTF275.lay';<br>
neighbour = ft_neighbourselection(cfg, Baseline{1});<br>
cfg = [];<br>
cfg.grad = TFR.grad;<br>
cfg.channel = {'MEG', '-MRO31', '-MRO21'};<br>
cfg.neighbourdist = 4;<br>
cfg.minnbchan = 1;<br>
cfg.clusteralpha = 0.05; % control admission to a cluster<br>
cfg.alpha = 0.05; % control the false alarm rate of the<br>
permutation test<br>
cfg.latency = [0.5 1.5]; % time interval over which the<br>
experimental conditions are compared (in sec)<br>
cfg.frequency = [50 70];<br>
cfg.avgovertime = 'no';<br>
cfg.avgoverfreq = 'no';<br>
cfg.avgoverchan = 'no';<br>
cfg.clusterstatistics = 'maxsum';<br>
cfg.statistic = 'actvsblT';<br>
cfg.numrandomization = 1000;<br>
cfg.correctm = 'cluster';<br>
cfg.method = 'montecarlo';<br>
cfg.approach = 'montecarlo';<br>
cfg.dimord = 'chan_freq_time';<br>
cfg.dim = 'chan_freq_time';<br>
cfg.neighbours = neighbour;<br>
cfg.tail = 0;<br>
cfg.clustertail = 0;<br>
<br>
nSubjects = 2*length(Controls);<br>
<br>
a = [1:nSubjects];<br>
b = ones(1,length(Controls));<br>
c = 2*(ones(1,length(Controls)));<br>
<br>
cfg.design = [a; b c];<br>
cfg.uvar = 1; % "subject" is unit of observation<br>
cfg.ivar = 2; % row of the design matrix that contains the independent<br>
variable<br>
<br>
stat = ft_freqstatistics(cfg, BaselineAll, StimuliAll);<br>
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<br>
Message: 3<br>
Date: Tue, 13 Sep 2011 11:00:13 +0200<br>
From: Roemer van der Meij <<a href="mailto:r.vandermeij@donders.ru.nl">r.vandermeij@donders.ru.nl</a>><br>
To: Email discussion list for the FieldTrip project<br>
<<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>><br>
Subject: Re: [FieldTrip] ft_freqstatistics issue (??? Undefined<br>
function or method 'randperm' for input arguments of type 'double'.)<br>
Message-ID: <<a href="mailto:4E6F1B9D.3050003@donders.ru.nl">4E6F1B9D.3050003@donders.ru.nl</a>><br>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"<br>
<br>
Hi Davide,<br>
<br>
It sounds like you are missing the Statistics Toolbo<br>
<<a href="http://www.mathworks.nl/products/statistics/index.html" target="_blank">http://www.mathworks.nl/products/statistics/index.html</a>>x for matlab. I<br>
remember some internal discussions in the team about writing an internal<br>
version of randperm.m with similar functions, but we haven't done so far<br>
if I recall correctly. Installing the toolbox, or checking whether you<br>
have it on your path should solve your problem.<br>
<br>
Hope it helps,<br>
Roemer<br>
<br>
<br>
<br>
On 13-09-11 9:38, Davide Rivolta wrote:<br>
> Dear fieldtrippers,<br>
> I wish to calculate the stat difference between stimulus and baseline<br>
> in a group of subjects. I use ft_freqgrandaverage to average across<br>
> subjects and then ft_freqstatistics (cluster statistic) to compare the<br>
> 2 conditions (baseline & stimuli).<br>
> I get this error: ??? Undefined function or method 'randperm' for<br>
> input arguments of type 'double'.<br>
> I tried even with the newest version (20110911) but the problem<br>
> persists. I am not sure what I have to do.<br>
> Any advice would be super. The script is below.<br>
> Thanks a lot,<br>
> Davide<br>
> datainpath = '/data/home1/drivolta/Out4VG/DATA/';<br>
> dataoutpath = '/data/home1/drivolta/Out4VG/DATA/';<br>
><br>
> % Controls<br>
> Controls = {<br>
> 'ASS31_TFR_high.mat';<br>
> 'CSA07_TFR_high.mat';<br>
> 'BMR08_TFR_high.mat';<br>
> 'NPD18_TFR_high.mat';<br>
> %'BSA08_TFR_high.mat';<br>
> %'ABE08_TFR_high.mat';<br>
> %'EES05_TFR_high.mat';<br>
> %'GPS10_TFR_high.mat';<br>
> %'SDA01_TFR_high.mat';<br>
> %'CSA17_TFR_high.mat';<br>
> %'KBZ16_TFR_high.mat';<br>
><br>
> };<br>
> %--------------------------------------------------------------------------<br>
> NControls = length(Controls);<br>
> %% CONCATENATE DATA<br>
> for i = 1:length(Controls)<br>
> fullname = strcat(datainpath, Controls{i,1});<br>
> load(fullname);<br>
><br>
> % Activation time window<br>
> TFR2 = power_continue_high; %Rename to change (select time window)<br>
> idx = find((TFR2.time >= 0.5) &(TFR2.time <= 1.5));<br>
> TFR2.powspctrm = power_continue_high.powspctrm(:, :,idx);<br>
> TFR2.time = power_continue_high.time(idx);<br>
> Stimuli{i} = TFR2;<br>
><br>
> % Baseline time window<br>
> TFR3 = power_continue_high;<br>
> idx = find((TFR3.time >= -1) &(TFR3.time < 0));<br>
> TFR3.powspctrm = power_continue_high.powspctrm(:,:, idx);<br>
> TFR3.time = TFR2.time;<br>
> Baseline{i} = TFR3;<br>
><br>
> clear power_continue_high<br>
> clear TFR2<br>
> clear TFR3<br>
> end;<br>
> save Controls2Statistics Stimuli Baseline;<br>
><br>
> cfg = [];<br>
> cfg.channel = {'MEG', '-MRO31', '-MRO21'};<br>
> cfg.keepindividual = 'yes';<br>
> BaselineAll = ft_freqgrandaverage(cfg, Baseline{:});<br>
> StimuliAll = ft_freqgrandaverage(cfg, Stimuli{:});<br>
> load /data/home1/drivolta/Out4VG/DATA/GRAD % File with a structure<br>
> containing grad field<br>
> cfg = [];<br>
> cfg.method = 'triangulation';<br>
> cfg.neighbourdist = 5;<br>
> cfg.grad = TFR.grad;<br>
> cfg.layout = 'CTF275.lay';<br>
> neighbour = ft_neighbourselection(cfg, Baseline{1});<br>
> cfg = [];<br>
> cfg.grad = TFR.grad;<br>
> cfg.channel = {'MEG', '-MRO31', '-MRO21'};<br>
> cfg.neighbourdist = 4;<br>
> cfg.minnbchan = 1;<br>
> cfg.clusteralpha = 0.05; % control admission to a cluster<br>
> cfg.alpha = 0.05; % control the false alarm rate of the<br>
> permutation test<br>
> cfg.latency = [0.5 1.5]; % time interval over which the<br>
> experimental conditions are compared (in sec)<br>
> cfg.frequency = [50 70];<br>
> cfg.avgovertime = 'no';<br>
> cfg.avgoverfreq = 'no';<br>
> cfg.avgoverchan = 'no';<br>
> cfg.clusterstatistics = 'maxsum';<br>
> cfg.statistic = 'actvsblT';<br>
> cfg.numrandomization = 1000;<br>
> cfg.correctm = 'cluster';<br>
> cfg.method = 'montecarlo';<br>
> cfg.approach = 'montecarlo';<br>
> cfg.dimord = 'chan_freq_time';<br>
> cfg.dim = 'chan_freq_time';<br>
> cfg.neighbours = neighbour;<br>
> cfg.tail = 0;<br>
> cfg.clustertail = 0;<br>
> nSubjects = 2*length(Controls);<br>
> a = [1:nSubjects];<br>
> b = ones(1,length(Controls));<br>
> c = 2*(ones(1,length(Controls)));<br>
> cfg.design = [a; b c];<br>
> cfg.uvar = 1; % "subject" is unit of observation<br>
> cfg.ivar = 2; % row of the design matrix that contains the independent<br>
> variable<br>
> stat = ft_freqstatistics(cfg, BaselineAll, StimuliAll);<br>
><br>
><br>
> _______________________________________________<br>
> fieldtrip mailing list<br>
> <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
<br>
--<br>
Roemer van der Meij M.Sc.<br>
PhD student<br>
Donders Institute for Brain, Cognition and Behaviour<br>
Centre for Cognition<br>
P.O. Box 9104<br>
6500 HE Nijmegen<br>
The Netherlands<br>
Tel: <a href="tel:%2B31%280%2924%203655932" value="+31243655932">+31(0)24 3655932</a><br>
E-mail: <a href="mailto:r.vandermeij@donders.ru.nl">r.vandermeij@donders.ru.nl</a><br>
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End of fieldtrip Digest, Vol 10, Issue 15<br>
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</blockquote></div><br>