[FieldTrip] Question on coherence stats at sensor level
Jörn M. Horschig
jorn at artinis.com
Thu Mar 3 15:00:58 CET 2016
Hi David,
If I remember correctly you can call ft_checkdata with the key-value
pair cmbrepresentation, full if you want to switch back from
data.labelcmb to data.label (or sparse for the reverse way).
Best,
Jörn
--
Jörn M. Horschig, PhD, Software Engineer
<http://www.artinis.com/> Artinis Medical Systems | +31 481 350 980
From: fieldtrip-bounces at science.ru.nl
[mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of David Pedrosa
Sent: Wednesday, March 2, 2016 12:39
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] Question on coherence stats at sensor level
Hi Jorn,
thanks for the fast help! It was as you suggested.
Now, I have a different issue someone might be able to help me with.
When I do the analyses as explained, fieldtrip tells me that cluster
stats are not possible as there are no labels in the data. This of
course makes sense as it is coherence data with a labelcmb instead of
label structure. Is there a way to do the cluster correction in
fieldtrip with coherence data anyway? Or would it make more sense to
take the raw fourier data into ft_freqstatistics and do the stats as
desired in a custom statfun function with the corrections as wanted,
e.g. similar to indepsamplesZcoh but for between subjects analyses?
Best
David
_____
Dr. David Pedrosa
Clinical Research Fellow
Medical Research Council Brain Network Dynamics Unit at the University
of Oxford
Nuffield Department of Clinical Neurosciences
University of Oxford
Level 6, West Wing
John Radcliffe Hospital, OX3 9DU
Tel: +44 (0)1865 572490
E-Mail: <mailto:david.pedrosa at ndcn.ox.ac.uk>
david.pedrosa at ndcn.ox.ac.uk
<https://owa.nexus.ox.ac.uk/owa/redir.aspx?C=E40BwPuNq0uXQGSOPDW39AmtYlw
BR9IIjsI0PRu9uuTE46jeZnqjmG6XP02rBAUiF1EnCJtn3UU.&URL=http%3a%2f%2fwww.m
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_____
Von: <mailto:fieldtrip-bounces at science.ru.nl>
fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]" im
Auftrag von "Jörn M. Horschig [jorn at artinis.com]
Gesendet: Dienstag, 1. März 2016 16:20
An: 'FieldTrip discussion list'
Betreff: Re: [FieldTrip] Question on coherence stats at sensor level
Hi David,
The problem is with specifying cfg.statistics = diff. the ft_xxxstats
function work by eval-ing the content of cfg.statistics. Thus, it runs
the built-in Matlab function diff, which is not defined for structs
such as FT-data variables, but only for matrices (and cells?).
I saw there is also a ft_statfun_diff, which is probably the one you
were aiming to use. The problem is that internally, the private
function ft_getuserfun is checking first for the existence of diff,
before it even comes to considering ft_statfun_diff. Long story short,
you can most likely solve your problem by specifying ft_statfun_diff
instead of diff, and the FT guys should think about what to do with
ft_getuserfun.
All the best,
Jörn
--
Jörn M. Horschig, PhD, Software Engineer
<http://www.artinis.com/> Artinis Medical Systems | +31 481 350 980
From: fieldtrip-bounces at science.ru.nl
<mailto:fieldtrip-bounces at science.ru.nl>
[mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of David Pedrosa
Sent: Tuesday, March 1, 2016 16:22
To: fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl>
Subject: [FieldTrip] Question on coherence stats at sensor level
Dear list,
I running analyses on the sensor level with EMG-EEG coherence data and I
ran into some problems. Basically my intention is to compare the
corticomuscular coherence at rest versus during an activation task. For
that, according to some older posts and literature, I computed the
Z-transformed coherence (after using ft_connectivityanalyses, I manually
transformed the cohspctrm data with respect to the dof) which I want to
test with a permutation test. Now, when it comes to computing the stats,
it gives me the error >> Function 'diff' is not supported for class
'struct'. << Would it be more reasonable using another function? Or does
anyone have an idea where my problem could be or what I should do
instead?
Here's the used code I use:
%% for loop normalizing coherence manually and creating
0-coherence data...
coh_diff{1,1} = coh_diff_condition{1,1}.cohspctrm =
(atanh(x1) - ...
coh_diff_null{1,1}.cohspctrm(:) = 0;
cfg = [];
cfg.channel = {'EEG' 'xEDC'};
cfg.parameter = 'cohspctrm';
cfg.method = 'montecarlo';
cfg.statistic = 'diff';
cfg.tail = 0;
cfg.clustertail = 0;
cfg.alpha = .025;
cfg.numrandomization = 500;
cfgl = [];
cfgl.layout = 'brainamp.sfp';
cfg.layout = ft_prepare_layout(cfgl);
cfg.computestat = 'yes';
cfg.correctm = 'cluster';
cfg.clusteralpha = .05;
cfg.clusterstatistic = 'maxsum';
cfg.minnbchan = 2;
cfgn = [];
cfgn.method = 'distance';
cfgn.neighbourdist = 40; %in mm
cfg.neighbours =
ft_prepare_neighbours(cfgn,data_epoched_wo);
design = zeros( 2,2*numel(coh_diff));
design(1,:) = [1:numel(coh_diff),
1:numel(coh_diff_null)];
design(2,1:numel(coh_diff)) = 1;
design(2,numel(coh_diff)+1:numel(coh_diff)+numel(coh_diff_null)) = 2;
cfg.design = design;
cfg.ivar = 1;
cfg.uvar = 2;
[stat] = ft_freqstatistics(cfg, coh_diff{1,1},
coh_diff{1,2}, ..., coh_diff_null{1,12};
Thanks for your help.
Best,
David
_____
Dr. David Pedrosa
Clinical Research Fellow
Medical Research Council Brain Network Dynamics Unit at the University
of Oxford
Nuffield Department of Clinical Neurosciences
University of Oxford
Level 6, West Wing
John Radcliffe Hospital, OX3 9DU
Tel: +44 (0)1865 572490
E-Mail: <mailto:david.pedrosa at ndcn.ox.ac.uk>
david.pedrosa at ndcn.ox.ac.uk
<https://owa.nexus.ox.ac.uk/owa/redir.aspx?C=E40BwPuNq0uXQGSOPDW39AmtYlw
BR9IIjsI0PRu9uuTE46jeZnqjmG6XP02rBAUiF1EnCJtn3UU.&URL=http%3a%2f%2fwww.m
rcbndu.ox.ac.uk%2f> http://www.mrcbndu.ox.ac.uk/
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