[FieldTrip] Source statistic issue - between trials

[Thomas Kustermann]

Hey Michał,

I think your problem lies within the use of "ft_statfun_depsamplesT".
FieldTrip then assumes that each trial index from condition one is paired
with the same trial index from condition two which is why you get the
output "repeated measurement in variable 2 over 11 levels
number of repeated measurements in each level is 2 2 2 2 2 2 2 2 2 2 1 "
In your case the design matrix should only include your first row and no
uvar, statfun being ft_statfun_indepsamplesT.
See: http://www.fieldtriptoolbox.org/tutorial/cluster_permutation
_freq#permutation_test

Cheers



On Tue, Jan 24, 2017 at 3:21 PM, Michał Komorowski <michak at is.umk.pl> wrote:

> Dear community,
>
> Currently I am working on source analysis from EEG data. I have some
> trouble using ft_sourcestatistics do a between-trials analysis (single
> subject).
> I am trying to compare source from trials from task type A (ctrl) to with
> trials from task type B (task). Mainly I rely on
> http://www.fieldtriptoolbox.org/example/source_statistics .
>
> For almost week I am trying find a solution, inculding testing
> ft_sourcestatistics with different combinations of data:
> 1) source 1 : no ft_sourcedescriptives and no ft_sourceinterpolate used
> 2) source 2 : used ft_sourcedescriptives and no ft_sourceinterpolate used
> 3) source 3 : used ft_sourcedescriptives and used ft_sourceinterpolate
>
> For cases 1) and 2) I get very similar errors "Invalid specification of
> the design array. Error using ft_statistics_montecarlo (line 242) could not
> determine the parametric critical value for clustering" (full error
> messages at the bottom). In case 3) I cannot run ft_statistics because
> there are no trials anymore.
> I have tried changing design matrix, search community messages for some
> advice and read related articles on fieldtriptoolbox site, but I have not
> find the answer.
>
> Any help would be appreciated.
>
> Michał Komorowski
>
>
> Statistics code:
>
> cfg = [];
> %cfg.dim         = source.dim; % there is no such field in the data
> cfg.method      = 'montecarlo';
> cfg.statistic   = 'ft_statfun_depsamplesT';
> cfg.parameter   = 'pow';
> cfg.correctm    = 'cluster';
> cfg.numrandomization = 100;
> cfg.alpha       = 0.05;
> cfg.correcttail = 'alpha'; % http://www.fieldtriptoolbox.or
> g/faq/why_should_i_use_the_cfg.correcttail_option_when_using
> _statistics_montecarlo
> cfg.tail        = 0; % two sided test
> cfg.design(1,:) = design; % condition code
> cfg.design(2,:) = [1:length(find(design==1)) 1:length(find(design==2))]; %
> trial indices
> cfg.uvar        = 2;  % unit of observation variable: trials
> cfg.ivar        = 1;  % independent variable: condition code
> % I think design matrix is ok according to: http://www.fieldtriptoolbox.or
> g/walkthrough#paired_comparison)
>
> stat = ft_sourcestatistics(cfg, source);
>
>
>
>
> Data structures and error messages
>
> Case 1) no ft_sourcedescriptives and no ft_sourceinterpolate used
>
> source =
>
>          freq: 10
>     cumtapcnt: [21x1 double]
>        inside: [231420x1 logical]
>           pos: [231420x3 double]
>        method: 'rawtrial'
>         trial: [1x21 struct]
>            df: 21
>           cfg: [1x1 struct]
>
> the call to "ft_selectdata" took 1 seconds
> using "ft_statistics_montecarlo" for the statistical testing
> using connectivity of voxels in 3-D volume
> using "ft_statfun_depsamplesT" for the single-sample statistics
> constructing randomized design
> total number of measurements     = 21
> total number of variables        = 2
> number of independent variables  = 1
> number of unit variables         = 1
> number of within-cell variables  = 0
> number of control variables      = 0
> using a permutation resampling approach
> repeated measurement in variable 2 over 11 levels
> number of repeated measurements in each level is 2 2 2 2 2 2 2 2 2 2 1
> computing a parametric threshold for clustering
> Error using ft_statfun_depsamplesT (line 84)
> Invalid specification of the design array.
> Error using ft_statistics_montecarlo (line 242)
> could not determine the parametric critical value for clustering
>
> Error in ft_sourcestatistics (line 205)
>   [stat, cfg] = statmethod(cfg, dat, design);
>
> >> cfg.design
>
> ans =
>
>      1     1     1     1     1     1     1     1     1     1     1     2
>   2     2     2     2     2     2     2     2     2
>      1     2     3     4     5     6     7     8     9    10    11     1
>   2     3     4     5     6     7     8     9    10
>
>
>
> Case 2) used ft_sourcedescriptives and no ft_sourceinterpolate used
>
> source_app =
>
>          freq: 10
>     cumtapcnt: [21x1 double]
>        inside: [231420x1 logical]
>           pos: [231420x3 double]
>        method: 'rawtrial'
>         trial: [1x21 struct]
>            df: 21
>           cfg: [1x1 struct]
>
> the call to "ft_selectdata" took 0 seconds
> using "ft_statistics_montecarlo" for the statistical testing
> using connectivity of voxels in 3-D volume
> using "ft_statfun_depsamplesT" for the single-sample statistics
> constructing randomized design
> total number of measurements     = 21
> total number of variables        = 2
> number of independent variables  = 1
> number of unit variables         = 1
> number of within-cell variables  = 0
> number of control variables      = 0
> using a permutation resampling approach
> repeated measurement in variable 2 over 11 levels
> number of repeated measurements in each level is 2 2 2 2 2 2 2 2 2 2 1
> computing a parametric threshold for clustering
> Error using ft_statfun_depsamplesT (line 84)
> Invalid specification of the design array.
> Error using ft_statistics_montecarlo (line 242)
> could not determine the parametric critical value for clustering
>
> Error in ft_sourcestatistics (line 205)
>   [stat, cfg] = statmethod(cfg, dat, design);
>
>
>
> Case 3) used ft_sourcedescriptives and used ft_sourceinterpolate
>
> source_mri_align_ctrl =
>
>          freq: 10
>       anatomy: [128x128x128 double]
>      coordsys: 'spm'
>           dim: [128 128 128]
>           pos: [2097152x3 double]
>     transform: [4x4 double]
>          unit: 'mm'
>        inside: [128x128x128 logical]
>           pow: [2097152x1 double]
>           cfg: [1x1 struct]
>
> % there is no trials so one cannot conduct between-trials statistics ...
>
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