[FieldTrip] regressconfound and frequency domain

Fri Feb 21 15:53:35 CET 2014

Dear Alik, If I am correct, you're asking how to create subject-level t-descriptives, mentioned in the previous post? A quick answer would be to perform an indepedent t-test ( cfg.statistic = indepsamplesT; ) using ft_timelockstatistics (although you're not really 'testing' here, but only interested in that t-descriptive), in which trials are the unit of observations ( cfg.design = [ones(1, ntrls_conditionA) 2*ones(1, ntrls_conditionB)]; ). Note that since an indepedent t-test tests for differences of the means of two conditions, it won't fail on unequal number of observations across the conditions (unlike a dependent/paired t-test). Hope this gets you kickstarted for the moment. I found a previous mail-conversation that goes more into detail, providing more overview of the steps involved: http://mailman.science.ru.nl/pipermail/fieldtrip/2011-November/004539.html More useful documentation: http://fieldtrip.fcdonders.nl/faq/what_is_the_idea_behind_statistical_inference_at_the_second-level Yours, Arjen ----- Oorspronkelijk bericht -----
> Van: "Alik Widge" <alik.widge at gmail.com>
> Aan: "FieldTrip discussion list" <fieldtrip at science.ru.nl>
> Verzonden: Vrijdag 21 februari 2014 11:38:10
> Onderwerp: Re: [FieldTrip] regressconfound and frequency domain
> Arjen, what you just described is more or less what I struggled to do
> last week and ultimately gave up as I was unable to figure out how to
> get FT to do it despite much meditation over tutorials and source
> files. Can you elaborate a bit more on what you are saying below --
> not the ft_regressconfound bit, but the bit about how to get
> ft_statistics_montecarlo and its wrappers to do a trials-level
> analysis and permutation at the whole-group level? Especially, what
> does one put in cfg.design and how does one call the function?
> Everything I could find in the tutorials described the case of doing
> means at the subject level and then permutation of means at the group
> level, which as you point out is underpowered for subtle effects.
> My particular situation was timelock-analyzed trials (with
> keeptrials='yes'), but I could not find a way to set up cfg.design
> that did not throw error messages. The thing that really seemed to
> bother it was that there were different numbers of trials in the 2-3
> conditions of interest, since some had to be removed for excessive
> artifact.
> Thanks for any help,
> Alik
> Alik Widge
> alik.widge at gmail.com
> (206) 866-5435
> On Fri, Feb 21, 2014 at 3:23 AM, Stolk, A. (Arjen) <
> a.stolk at fcdonders.ru.nl > wrote:
> > Dear Raghavan,
> > To compute a t-descriptive on subject level freq data, you'll need
> > to
> > use ft_freqstatistics. Have a look here for instance:
> > http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq
> > At the subject level, you do not need (non-parametric) cluster
> > permutation testing (Maris & Oostenveld), as you're taking each
> > subject's t-descriptives to the group level. At the group level, you
> > can then test the hypothesis that there's a difference between
> > tasks/conditions (H1) vs. no difference (H0). In order to do so,
> > you'll need to create a dummy variable at the group level, that has
> > the same number of 'subjects', but with zeros in all fields (in your
> > case this will be a .stat field). At the group level, you thus call
> > ft_freqstatistics again. This approach has the advantage that you're
> > more sensitive (as compared to taking each subject's mean to the
> > group
> > level) to effects that are small but consistent over trials in each
> > subject.
> > Arjen
> > > Van: "Raghavan Gopalakrishnan" < gopalar.ccf at gmail.com >
> > > Aan: fieldtrip at science.ru.nl
> > > Verzonden: Donderdag 20 februari 2014 23:33:18
> > > Onderwerp: Re: [FieldTrip] regressconfound and frequency domain
> > > Thanks Arjen,
> > > Should I use ft_freqdescriptives to compute t descriptives for
> > > individual subjects, and then take that to group level instead of
> > > mean? If not, what are the other alternatives?
> > > Thanks,
> > > Raghavan
> > > Hi Raghavan, ft_regressconfound run on timelock data seems to
> > > return
> > > output with avg field. However, ft_regressconfound run on
> > > frequency
> > > data, does not return average. I see the avg field being removed.
> > > Is
> > > there a reason? >> Not intentionally, but not an issue either. You
> > > could still use ft_freqdescriptives to compute the average for
> > > you,
> > > but see my comment below. Question - Since ft_regressconfound
> > > outputs
> > > power spectrum of individual trials - 4D matrix (instead of
> > > average),
> > > can I simply re-average the power spectrum over trials to see the
> > > average power for that subject. Also, I need to run grand average
> > > (over subjects) before running statistics. I hope these steps does
> > > not
> > > distort the data. Please advise. >> Remember that the mean over
> > > trials
> > > is not affected by your clean-up of trial-by-trial variance due to
> > > head movement. Taking each subject's mean (unaffected) to the
> > > group
> > > level is an approach that will not benefit from your clean-up. In
> > > order to benefit from reduced trial-by-trial variance, you'll need
> > > a
> > > measure that depends on it, e.g. t-descriptive, neural
> > > activity-behavior correlation (for taking to the group level).
> > > Hope
> > > this helps, Arjen ----- Oorspronkelijk bericht -----
> > > > Van: "Raghavan Gopalakrishnan" < gopalar.ccf at gmail.com > >
> > > > Aan:
> > > > fieldtrip at science.ru.nl > Verzonden: Donderdag 20 februari
> > > > 2014
> > > > 22:12:28 > Onderwerp: Re: [FieldTrip] regressconfound and
> > > > frequency
> > > > domain > Arjen, > Thanks, I reduced down the time resolution so
> > > > computation can go > faster. Now, m y matrix looks like this >
> > > > hpicomptimefreq = > label: {204x1 cell} > dimord:
> > > > 'rpt_chan_freq_time' > freq: [1x56 double] > time: [1x375
> > > > double]
> > > > >
> > > > powspctrm: [4-D double] > cumtapcnt: [59x56 double] > cfg: [1x1
> > > > struct] > trialinfo: [59x1 double] > beta: [4-D double] >
> > > > ft_regressconfound run on timelock data seems to return output
> > > > with
> > > > > avg field. However, ft_regressconfound run on frequency data,
> > > > > does
> > > > not > return average. I see the avg field being removed. Is
> > > > there
> > > > a
> > > > reason? > Question - Since ft_regressconfound outputs power
> > > > spectrum
> > > > of > individual trials - 4D matrix (instead of average), can I
> > > > simply > re-average the power spectrum over trials to see the
> > > > average power for > that subject. Also, I need to run grand
> > > > average
> > > > (over subjects) before > running statistics. I hope these steps
> > > > does
> > > > not distort the data. > Please advise. > Thanks, > Raghavan >
> > > > Date:
> > > > Wed, 19 Feb 2014 22:58:38 +0100 (CET) > From: "Stolk, A.
> > > > (Arjen)"
> > > > <
> > > > a.stolk at fcdonders.ru.nl > > To: FieldTrip discussion list <
> > > > fieldtrip at science.ru.nl > > Subject: Re: [FieldTrip]
> > > > regressconfound and frequency domain > Message-ID: > <
> > > > 2108167665.5423215.1392847118322.JavaMail.root at
> > > > sculptor.zimbra.ru.nl > > > Content-Type: text/plain;
> > > > charset="utf-8" > Dear Raghavan, Good to hear it's working out
> > > > for
> > > > you. A short answer > would be 'no'. Reducing the size of your
> > > > data
> > > > matrix is likely going > to speed up computations. Your time
> > > > resolution seems pretty high (1500 > frequency estimations per
> > > > single trial); do you need that many? Yours, > Arjen -----
> > > > Oorspronkelijk bericht ----- > > Van: "Raghavan Gopalakrishnan"
> > > > <
> > > > gopalar.ccf at gmail.com > > > Aan: fieldtrip at science.ru.nl >
> > > > >
> > > > Verzonden: Woensdag 19 februari 2014 22:01:00 > > Onderwerp:
> > > > [FieldTrip] regressconfound and frequency domain > > Arjen, > >
> > > > Thanks for answering all my previous questions. I was
> > > > successfully
> > > > >
> > > > > able to incorporate head movements to my erf data. As I
> > > > > understand
> > > > I > > have to do this separately for the time frequency data
> > > > after
> > > > keeping > > individual trials. I am interested in both beta and
> > > > gamma bands > > [15:1:70]. my time frequency looks like this
> > > > using
> > > > wavelets, > > timefreq = > > label: {204x1 cell} > > dimord:
> > > > 'rpt_chan_freq_time' > > freq: [1x56 double] > > time: [1x1500
> > > > double] > > powspctrm: [4-D double] > > cumtapcnt: [55x56
> > > > double]
> > > > >
> > > > > grad: [1x1 struct] > > elec: [1x1 struct] > > cfg: [1x1
> > > > > struct]
> > > > > >
> > > > > trialinfo: [55x1 double] > > After regressconfound > >
> > > > hpicomptimefreq = > > label: {204x1 cell} > > dimord:
> > > > 'rpt_chan_freq_time' > > freq: [1x56 double] > > time: [1x1500
> > > > double] > > powspctrm: [4-D double] > > cumtapcnt: [55x56
> > > > double]
> > > > >
> > > > > cfg: [1x1 struct] > > trialinfo: [55x1 double] > > beta: [4-D
> > > > double] > > Regressconfound took about 1 hr and 30 mins, since
> > > > its
> > > > a
> > > > huge matrix > > [55x204x56x1500]. I have 25 such blocks of data
> > > > for
> > > > 20 subjects. It > > will take an enoumous amount of time to
> > > > process
> > > > the data through > > regressconfound. Is there a workaround to
> > > > make
> > > > the processing faster > > or am I missing something. Any help
> > > > would
> > > > be of great help. > > Thanks, > > Raghavan
> > > _______________________________________________
> > > fieldtrip mailing list
> > > fieldtrip at donders.ru.nl
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > --
> > Donders Institute for Brain, Cognition and Behaviour
> > Centre for Cognitive Neuroimaging
> > Radboud University Nijmegen
> > Email: a.stolk at donders.ru.nl
> > Phone: +31(0)243 68294
> > Web: www.arjenstolk.nl
> > _______________________________________________
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> > fieldtrip at donders.ru.nl
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-- Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Email: a.stolk at donders.ru.nl Phone: +31(0)243 68294 Web: www.arjenstolk.nl
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