[FieldTrip] source statistics - spm_bwlabel error

[Schoffelen, J.M. (Jan Mathijs)]

Hi Malgorzata,

Could you try to add the original ‘tri’ field to each of your varargins, and check whether the problem persists?

Thanks,
Jan-Mathijs



On 26 May 2017, at 11:52, Malgorzata Wislowska <malgorzata.wislowska at gmail.com<mailto:malgorzata.wislowska at gmail.com>> wrote:

Dear Julian,


thank you very much for your prompt response.

Yes, my numdims == 2 because my cfg.dim == [8196 1]
which comes from ft_sourcestatistics.m (code lines 131-132)
datdim = find(~strcmp(dimtok, 'subj') & ~strcmp(dimtok, 'rpt') & ~strcmp(dimtok, 'rpttap'));
datsiz = dimsiz(datdim);
calculated on the following input data:
varargin{1}:
       cfg: [1x1 struct]
    inside: [8196x1 logical]
       pos: [8196x3 double]
      time: 0.1750
       pow: [8196x1 double]
    dimord: 'chan_time'
The above source level structure comes from ft_sourceanalysis calculated with cfg.method = 'mne'.

Averaging over time unfortunately doesn't help - the same error continues to occur:
But data that is not averaged over time has numdims == 2 too, because length(cfg.dim) == 2, even though that cfg.dim itself is different (for not averaged data it's e.g cfg.dim == [8196 61], whereas for averaged data it's cfg.dim == [8196 1]),

It helps (well, the function runs through without errors and produces some output) if the line:
if numdims == 2 || numdims == 3 % if 2D or 3D data
gets replaced with:
if numdims == 3
In clusterstat.m, code line: 318 (and also 269, 215, 184)

Do you (or anybody else) have maybe any better idea how to fix it?


Thanks and best regards,
Malgorzata,
University Salzburg



Subject: Re: [FieldTrip] source statistics - spm_bwlabel error

Dear Malgorzata,

from a quick glance, it appears that in the call to spm_bwlabel "numdims" should be 3 to give you 2*numdims = 6.
So, could you check what numdims is in your case?
I suspect that you have 4-dimensional data (time by 3 spatial dimensions), so it might help to check where the dimensions are coming from and what happens if you average over time.

Good luck,

Julian

Am 24.05.2017 um 16:34 schrieb Malgorzata Wislowska:

Dear FT-community,


when calculating cluster permutation statistics on the source level, I receive the following error:
Error using spm_bwlabel
spm_bwlabel: CONN must be 6, 18 or 26

Error in clusterstat (line 319)
        [negclusrnd, negrndnum] = spm_bwlabel(tmp, 2*numdims); % use spm_bwlabel for 2D/3D to avoid usage of image toolbox

Error in ft_statistics_montecarlo (line 347)
  [stat, cfg] = clusterstat(cfg, statrand, statobs);

Error in ft_sourcestatistics (line 218)
  [stat, cfg] = statmethod(cfg, dat, design);

I used MNE method for the inverse problem. I have 8196 grid points 1555 time points.
But the error occurs also when I average across the time.

Here is my configuration structure for the source analysis:

design          = zeros(2, nb_of_sbj*2);
design(1,:)   = [1:nb_of_sbj 1:nb_of_sbj];
design(2,:)     = [ones(1,nb_of_sbj) ones(1,nb_of_sbj)*2];

cfg                     = [];
cfg.method              = 'montecarlo';
cfg.statistic           = 'ft_statfun_depsamplesT';
cfg.parameter           = 'pow';
cfg.correctm            = 'cluster';
cfg.clusterstatistic    = 'maxsum';
cfg.design              = design;
cfg.ivar                = 2;
cfg.uvar                = 1;
cfg.numrandomization    = 5000;
cfg.tail                = 0;
cfg.alpha               = 0.025;

[stat]                  = ft_sourcestatistics(cfg,avg_con_sel{:},avg_incon_sel{:});

As far as I can see somebody had asked the same question last year, but the post doesn't seem to have been addressed:
https://mailman.science.ru.nl/pipermail/fieldtrip/2016-August/010762.html


Thank you for your help in advance.

Best regards,
Malgorzata Wislowska,
University of Salzburg
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