[FieldTrip] fieldtrip Digest, Vol 10, Issue 15
Anna Lambrechts
anna.lambrechts at gmail.com
Tue Sep 13 11:11:49 CEST 2011
Dear David,
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.
Best,
Anna.
2011/9/13 <fieldtrip-request at donders.ru.nl>
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> Today's Topics:
>
> 1. bufferviewer C++ code (JustinChen)
> 2. ft_freqstatistics issue (??? Undefined function or method
> 'randperm' for input arguments of type 'double'.) (Davide Rivolta)
> 3. Re: ft_freqstatistics issue (??? Undefined function or method
> 'randperm' for input arguments of type 'double'.)
> (Roemer van der Meij)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 12 Sep 2011 18:07:36 -0400
> From: JustinChen <justin.sickkids at hotmail.com>
> To: <fieldtrip at donders.ru.nl>
> Subject: [FieldTrip] bufferviewer C++ code
> Message-ID: <BAY152-W1973669968BE6CA059B9EFF9020 at phx.gbl>
> Content-Type: text/plain; charset="gb2312"
>
>
>
>
>
> 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
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> ------------------------------
>
> Message: 2
> Date: Tue, 13 Sep 2011 09:38:49 +0200
> From: Davide Rivolta <drivolta81 at gmail.com>
> To: fieldtrip at donders.ru.nl
> Subject: [FieldTrip] ft_freqstatistics issue (??? Undefined function
> or method 'randperm' for input arguments of type 'double'.)
> Message-ID:
> <CAMkcSw7VcTOp6rHZhFCyWxWFTwZ6BJTbNH5wgbuhTDh6W9Mbkg at mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear fieldtrippers,
>
> I wish to calculate the stat difference between stimulus and baseline in a
> group of subjects. I use ft_freqgrandaverage to average across subjects and
> then ft_freqstatistics (cluster statistic) to compare the 2 conditions
> (baseline & stimuli).
>
> I get this error: ??? Undefined function or method 'randperm' for input
> arguments of type 'double'.
>
> I tried even with the newest version (20110911) but the problem persists. I
> am not sure what I have to do.
>
> Any advice would be super. The script is below.
>
> Thanks a lot,
>
> Davide
>
>
>
> datainpath = '/data/home1/drivolta/Out4VG/DATA/';
> dataoutpath = '/data/home1/drivolta/Out4VG/DATA/';
>
> % Controls
> Controls = {
> 'ASS31_TFR_high.mat';
> 'CSA07_TFR_high.mat';
> 'BMR08_TFR_high.mat';
> 'NPD18_TFR_high.mat';
> %'BSA08_TFR_high.mat';
> %'ABE08_TFR_high.mat';
> %'EES05_TFR_high.mat';
> %'GPS10_TFR_high.mat';
> %'SDA01_TFR_high.mat';
> %'CSA17_TFR_high.mat';
> %'KBZ16_TFR_high.mat';
>
> };
>
> %--------------------------------------------------------------------------
> NControls = length(Controls);
>
> %% CONCATENATE DATA
> for i = 1:length(Controls)
> fullname = strcat(datainpath, Controls{i,1});
> load(fullname);
>
> % Activation time window
> TFR2 = power_continue_high; %Rename to change (select time window)
> idx = find((TFR2.time >= 0.5) &(TFR2.time <= 1.5));
> TFR2.powspctrm = power_continue_high.powspctrm(:, :,idx);
> TFR2.time = power_continue_high.time(idx);
> Stimuli{i} = TFR2;
>
> % Baseline time window
> TFR3 = power_continue_high;
> idx = find((TFR3.time >= -1) &(TFR3.time < 0));
> TFR3.powspctrm = power_continue_high.powspctrm(:,:, idx);
> TFR3.time = TFR2.time;
> Baseline{i} = TFR3;
>
> clear power_continue_high
> clear TFR2
> clear TFR3
> end;
> save Controls2Statistics Stimuli Baseline;
>
>
>
> cfg = [];
> cfg.channel = {'MEG', '-MRO31', '-MRO21'};
> cfg.keepindividual = 'yes';
>
> BaselineAll = ft_freqgrandaverage(cfg, Baseline{:});
> StimuliAll = ft_freqgrandaverage(cfg, Stimuli{:});
>
>
>
> load /data/home1/drivolta/Out4VG/DATA/GRAD % File with a structure
> containing grad field
>
> cfg = [];
> cfg.method = 'triangulation';
> cfg.neighbourdist = 5;
> cfg.grad = TFR.grad;
> cfg.layout = 'CTF275.lay';
> neighbour = ft_neighbourselection(cfg, Baseline{1});
> cfg = [];
> cfg.grad = TFR.grad;
> cfg.channel = {'MEG', '-MRO31', '-MRO21'};
> cfg.neighbourdist = 4;
> cfg.minnbchan = 1;
> cfg.clusteralpha = 0.05; % control admission to a cluster
> cfg.alpha = 0.05; % control the false alarm rate of the
> permutation test
> cfg.latency = [0.5 1.5]; % time interval over which the
> experimental conditions are compared (in sec)
> cfg.frequency = [50 70];
> cfg.avgovertime = 'no';
> cfg.avgoverfreq = 'no';
> cfg.avgoverchan = 'no';
> cfg.clusterstatistics = 'maxsum';
> cfg.statistic = 'actvsblT';
> cfg.numrandomization = 1000;
> cfg.correctm = 'cluster';
> cfg.method = 'montecarlo';
> cfg.approach = 'montecarlo';
> cfg.dimord = 'chan_freq_time';
> cfg.dim = 'chan_freq_time';
> cfg.neighbours = neighbour;
> cfg.tail = 0;
> cfg.clustertail = 0;
>
> nSubjects = 2*length(Controls);
>
> a = [1:nSubjects];
> b = ones(1,length(Controls));
> c = 2*(ones(1,length(Controls)));
>
> cfg.design = [a; b c];
> cfg.uvar = 1; % "subject" is unit of observation
> cfg.ivar = 2; % row of the design matrix that contains the independent
> variable
>
> stat = ft_freqstatistics(cfg, BaselineAll, StimuliAll);
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> ------------------------------
>
> Message: 3
> Date: Tue, 13 Sep 2011 11:00:13 +0200
> From: Roemer van der Meij <r.vandermeij at donders.ru.nl>
> To: Email discussion list for the FieldTrip project
> <fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] ft_freqstatistics issue (??? Undefined
> function or method 'randperm' for input arguments of type 'double'.)
> Message-ID: <4E6F1B9D.3050003 at donders.ru.nl>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hi Davide,
>
> It sounds like you are missing the Statistics Toolbo
> <http://www.mathworks.nl/products/statistics/index.html>x for matlab. I
> remember some internal discussions in the team about writing an internal
> version of randperm.m with similar functions, but we haven't done so far
> if I recall correctly. Installing the toolbox, or checking whether you
> have it on your path should solve your problem.
>
> Hope it helps,
> Roemer
>
>
>
> On 13-09-11 9:38, Davide Rivolta wrote:
> > Dear fieldtrippers,
> > I wish to calculate the stat difference between stimulus and baseline
> > in a group of subjects. I use ft_freqgrandaverage to average across
> > subjects and then ft_freqstatistics (cluster statistic) to compare the
> > 2 conditions (baseline & stimuli).
> > I get this error: ??? Undefined function or method 'randperm' for
> > input arguments of type 'double'.
> > I tried even with the newest version (20110911) but the problem
> > persists. I am not sure what I have to do.
> > Any advice would be super. The script is below.
> > Thanks a lot,
> > Davide
> > datainpath = '/data/home1/drivolta/Out4VG/DATA/';
> > dataoutpath = '/data/home1/drivolta/Out4VG/DATA/';
> >
> > % Controls
> > Controls = {
> > 'ASS31_TFR_high.mat';
> > 'CSA07_TFR_high.mat';
> > 'BMR08_TFR_high.mat';
> > 'NPD18_TFR_high.mat';
> > %'BSA08_TFR_high.mat';
> > %'ABE08_TFR_high.mat';
> > %'EES05_TFR_high.mat';
> > %'GPS10_TFR_high.mat';
> > %'SDA01_TFR_high.mat';
> > %'CSA17_TFR_high.mat';
> > %'KBZ16_TFR_high.mat';
> >
> > };
> >
> %--------------------------------------------------------------------------
> > NControls = length(Controls);
> > %% CONCATENATE DATA
> > for i = 1:length(Controls)
> > fullname = strcat(datainpath, Controls{i,1});
> > load(fullname);
> >
> > % Activation time window
> > TFR2 = power_continue_high; %Rename to change (select time window)
> > idx = find((TFR2.time >= 0.5) &(TFR2.time <= 1.5));
> > TFR2.powspctrm = power_continue_high.powspctrm(:, :,idx);
> > TFR2.time = power_continue_high.time(idx);
> > Stimuli{i} = TFR2;
> >
> > % Baseline time window
> > TFR3 = power_continue_high;
> > idx = find((TFR3.time >= -1) &(TFR3.time < 0));
> > TFR3.powspctrm = power_continue_high.powspctrm(:,:, idx);
> > TFR3.time = TFR2.time;
> > Baseline{i} = TFR3;
> >
> > clear power_continue_high
> > clear TFR2
> > clear TFR3
> > end;
> > save Controls2Statistics Stimuli Baseline;
> >
> > cfg = [];
> > cfg.channel = {'MEG', '-MRO31', '-MRO21'};
> > cfg.keepindividual = 'yes';
> > BaselineAll = ft_freqgrandaverage(cfg, Baseline{:});
> > StimuliAll = ft_freqgrandaverage(cfg, Stimuli{:});
> > load /data/home1/drivolta/Out4VG/DATA/GRAD % File with a structure
> > containing grad field
> > cfg = [];
> > cfg.method = 'triangulation';
> > cfg.neighbourdist = 5;
> > cfg.grad = TFR.grad;
> > cfg.layout = 'CTF275.lay';
> > neighbour = ft_neighbourselection(cfg, Baseline{1});
> > cfg = [];
> > cfg.grad = TFR.grad;
> > cfg.channel = {'MEG', '-MRO31', '-MRO21'};
> > cfg.neighbourdist = 4;
> > cfg.minnbchan = 1;
> > cfg.clusteralpha = 0.05; % control admission to a cluster
> > cfg.alpha = 0.05; % control the false alarm rate of the
> > permutation test
> > cfg.latency = [0.5 1.5]; % time interval over which the
> > experimental conditions are compared (in sec)
> > cfg.frequency = [50 70];
> > cfg.avgovertime = 'no';
> > cfg.avgoverfreq = 'no';
> > cfg.avgoverchan = 'no';
> > cfg.clusterstatistics = 'maxsum';
> > cfg.statistic = 'actvsblT';
> > cfg.numrandomization = 1000;
> > cfg.correctm = 'cluster';
> > cfg.method = 'montecarlo';
> > cfg.approach = 'montecarlo';
> > cfg.dimord = 'chan_freq_time';
> > cfg.dim = 'chan_freq_time';
> > cfg.neighbours = neighbour;
> > cfg.tail = 0;
> > cfg.clustertail = 0;
> > nSubjects = 2*length(Controls);
> > a = [1:nSubjects];
> > b = ones(1,length(Controls));
> > c = 2*(ones(1,length(Controls)));
> > cfg.design = [a; b c];
> > cfg.uvar = 1; % "subject" is unit of observation
> > cfg.ivar = 2; % row of the design matrix that contains the independent
> > variable
> > stat = ft_freqstatistics(cfg, BaselineAll, StimuliAll);
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> --
> Roemer van der Meij M.Sc.
> PhD student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognition
> P.O. Box 9104
> 6500 HE Nijmegen
> The Netherlands
> Tel: +31(0)24 3655932
> E-mail: r.vandermeij at donders.ru.nl
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> End of fieldtrip Digest, Vol 10, Issue 15
> *****************************************
>
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