[FieldTrip] Clusterplot with F-test

Stephen Politzer-Ahles politzerahless at gmail.com
Thu Oct 6 13:33:05 CEST 2011


Karl,

I believe you can accomplish the same thing as ft_clusterplot using the code
sample at
http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock#plotting_the_results1,
which also gives you the option to plot negative or positive clusters (or
both, if you fiddle with that code; there is a sample higher up on the page
that plots both).

Best,
Steve Politzer-Ahles

Message: 2
> Date: Wed, 5 Oct 2011 15:50:01 -0700
> From: Karl Doron <karl.doron at gmail.com>
> To: fieldtrip at donders.ru.nl
> Subject: [FieldTrip] Clusterplot with F-test
> Message-ID: <AE6D70A8-4C39-4400-909B-250ECDB34755 at gmail.com>
> Content-Type: text/plain; charset=us-ascii
>
> Hello,
>
> I've run a statistical analysis with cfg.statistic=depsamplesF. The tail of
> the F distribution is a one-sided test, so no negative cluster distributions
> are output as part of the processing. The clusterplot function seems to want
> negative clusters however. Is there any way around this?
>
> Best,
>
> karl
>
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 6 Oct 2011 16:54:43 +1100
> From: Tommy Ng <tommy.ng at mq.edu.au>
> To: fieldtrip at donders.ru.nl
> Subject: Re: [FieldTrip] Units for Y axis
> Message-ID:
>        <CABXsOyzauxDv__4a=neC_GubdCXbmqaFKPrOoe5k9cm1+HvZhA at mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear FT Experts
>
> I am very new to FT and would like to ask a simple question.
>
> Using FT beamformer source extraction module implemented in SPM8, I
> obtained
> time series of virtual sensors in source space. However, I do not know what
> is the unit for the Y axis.
>
> Can someone please advise?
>
> Thank you in advance.
>
> Tommy Ng
> PhD Student
> Macquarie University
> Australia
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> Message: 4
> Date: Thu, 6 Oct 2011 10:13:41 +0200
> From: <B.Mouthaan at neuro.umcn.nl>
> To: <fieldtrip at donders.ru.nl>
> Subject: [FieldTrip] Problems using .elp files
> Message-ID: <C1B628236A6B6B4AA11AE3022559568494D9B6 at UMCEXBE04.umcn.nl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Fieldtrippers,
>
> I am using .avr files for source modelling on ERP data. From the ERP
> components, I have calculated the differencewaves in a .mat file. Until this
> it all went fine. However I get stuck at using .elp files.
> I can succesfully create the headmodel with
> ft_prepare_singleshell(cfg,segementedmri) with the semi-realistic head model
> developed by Nolte (2003)
> However when using ft_prepare_leadfield(cfg) I get problems.
>
> My code is like this:
>
> % discretize brainvolume in grid
> cfg=[]
> cfg.inputfile= 'C:\Users\Brian\Documents\MATLAB\AnalysisM\differencewave01'
> [lbl] = importdata([subjectdata.subjectdir filesep subjectdata.electrodes])
> % reading in .elp files
>
> %renaming lbl.textdata to lbl.label, else it gives an error at
> ft_channelselection, because it is unable to read sens.label
> oldField = 'textdata';
> newField = 'label';
> [lbl.(newField)] = lbl.(oldField);
> lbl = rmfield(lbl,oldField);
> cfg.elec= lbl
> cfg.vol            = vol;
> cfg.reducerank      = 3;
> cfg.channel         = 'Fz'
> cfg.grid.resolution = 1;   % use a 3-D grid with a 1 cm resolution
> save cfg
> [grid] = ft_prepare_leadfield(cfg);
>
> When executing this I get the following commandscreen:
> ....
> .....
> using headmodel specified in the configuration
> using electrodes specified in the configuration
> ??? Error using ==> ft_prepare_vol_sens at 110
> the input does not look like EEG, nor like MEG
>
> Error in ==> prepare_headmodel at 114
> [vol, sens] = ft_prepare_vol_sens(vol, sens, 'channel', cfg.channel,
> 'order', cfg.order);
>
> Error in ==> ft_prepare_leadfield at 159
> [vol, sens, cfg] = prepare_headmodel(cfg, data);
>
> I think this is because I use .elp files? The .elp files contain N rows and
> 3 columns representing xyz or spherical coordinates I assume. However this
> is the only information I have about the electrodes, so I have to do with
> it.
>
> Any ideas?
>
> Kind regards,
>
> Brian
>
>
>
>
>
>
> Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het
> handelsregister onder nummer 41055629.
> The Radboud University Nijmegen Medical Centre is listed in the Commercial
> Register of the Chamber of Commerce under file number 41055629.
>
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> End of fieldtrip Digest, Vol 11, Issue 7
> ****************************************
>



-- 
Stephen Politzer-Ahles
University of Kansas
Linguistics Department
http://www.linguistics.ku.edu/
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