[FieldTrip] source statistics with ROI yields NaN clusters

Thu Oct 17 10:30:46 CEST 2013

Hi Roey and Joern,

Joern, my subjects' data are interpolated to the MNI template, as far as I
understand. I'm using a code that Jan-Mathijs and I worked on some time
ago, so what I'm doing should be really close to what's in the tutorial.
The only thing I can tell that is in the tutorial but not in my code is the
following:
"After that you should put .pos, .xgrid, .ygrid, .zgrid, .dim field from
the template_grid onto the subjects's source, which is thereby in MNI
coordinates."
In my code, we only copied .pos and .dim from the template to the subjects,
but not .xgrid, .ygrid, .zgrid. Would that explain the error?
I think I was using an FT version from the beginning of October when I got
the error (running in my PC, so not the DCCN's... sorry, I cannot look that
up now). When were the changes made you are referring to? I could look up
which version I was using (sorry for missing this very crucial information
in my last email), but it might as well be the case, as you mentioned, that
Roey and I are the first ones to try it out in this particular way ;)
Let me know if you need more info. Btw, I have these data in a hard disk at
the DCCN if you need to have a look.

Roey, yes, I'm using an MNI grid per subject (similar to the tutorial:
http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space>
Make the individual subjects' grid).

Cheers, Vitoria

> ------------------------------
>
> Message: 3
> Date: Wed, 16 Oct 2013 20:10:20 +0300
> From: Roey <roeysc at gmail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] source statistics with ROI yields NaN
> clusters
> Message-ID: <FF996E6D-BAEF-458D-BB41-B9CF1FC5B1DA at gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Vitoria and everyone else,
>
> I agree with J?rn (thank you!) , indeed it seems this is the same
> problem. Hopefully I'll get back to it next week and maybe figure it
> out. Right now it seems like the A side consists of all the
> inside-voxels, whereas the B side consists of the different ROIs, and
> hence the mismatch.
>
> A possible solution could be having the atlas we are using available
> to that function, and translating the B side to the voxel space.
>
> By the way, are you using an MNI grid per subject?
>
> Best,
> roey
>
>
>
> ?-16 ???? 2013, ???? 17:07, "J?rn M. Horschig"
> <jm.horschig at donders.ru.nl> ???/?:
>
> > Hi Vitoria,
> >
> > I guess that is the same error that Roey Schurr described a few days
> > back. There were some changes recently in the atlas lookup function
> > (we replaced one function and made another more general). Apparently
> > that broke some things, or you two just happen to do this as the
> > first ever ;)
> > The only thing I can think of is that you might need to interpolate
> > to the MNI template so that the dimensions are matched between the
> > atlas and your source structures. Could you give that a try and let
> > us know whether that helps?
> >
> > Best,
> > J?rn
> >
> >
> > On 10/16/2013 11:19 AM, Vit?ria Magalh?es Piai wrote:
> >> Dear all,
> >>
> >> I'm trying to run ft_sourcestatistics with a specified ROI. It's
> >> data (MNEs) averaged over time.
> >>
> >> If I run ft_sourcestatistics without an ROI, I get a cluster with
> >> prob = .178. It looks like this (figure attached), where I masked
> >> using the t-values.
> >> Since I'm dealing with an N400-like component, I've got good
> >> reasons to expect the effect to be localised (mainly) to left
> >> temporal areas.
> >>
> >> So I tried adding this to my cfg:
> >>
> >> cfgst.atlas = 'aal\ROI_MNI_V4.nii';
> >> cfgst.roi = {'Temporal_Mid_L' 'Temporal_Sup_L' 'Temporal_Inf_L' };
> >> cfgst.avgoverroi = 'yes';
> >> cfgst.hemisphere = 'left';
> >> cfgst.inputcoord = 'mni' ;
> >> stat = ft_sourcestatistics(cfgst, iRel{:}, iIde{:});
> >>
> >> If cfgst.avgoverroi == 'yes'; I get the following error:
> >>
> >> ??? In an assignment A(:) = B, the number of elements in A and B
> >> must be the same.
> >> Error in ==> clusterstat at 187
> >>     tmp(cfg.inside) = postailobs;
> >> Error in ==> ft_statistics_montecarlo at 326
> >>   [stat, cfg] = clusterstat(cfg, statrand,
> >>   statobs,'issource',issource);
> >> Error in ==> statistics_wrapper at 298
> >>     [stat, cfg] = statmethod(cfg, dat, design,
> >>     'issource',issource);
> >> Error in ==> ft_sourcestatistics at 107
> >>     [stat, cfg] = statistics_wrapper(cfg, varargin{:});
> >>
> >> If cfgst.avgoverroi == 'no';
> >> ft outputs "found positive clusters in observed data" and
> >> stat.posclusters/negclusters is only NaN. This is regardless of
> >> whether cfgst.roi is one label or a cell array.
> >>
> >> Does anyone know what I'm doing wrong?
> >> I've been completely stuck on source statistics for these MNEs for
> >> days, so any help would be highly appreciated, even if it is to
> >> suggest another way to do the stats!
> >>
> >> Thanks a lot, Vit?ria
> >>
> >>
> >> _______________________________________________
> >> fieldtrip mailing list
> >> fieldtrip at donders.ru.nl
> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> >
> > --
> > J?rn M. Horschig
> > PhD Student
> > Donders Institute for Brain, Cognition and Behaviour
> > Centre for Cognitive Neuroimaging
> > Radboud University Nijmegen
> > Neuronal Oscillations Group
> > FieldTrip Development Team
> >
> > P.O. Box 9101
> > NL-6500 HB Nijmegen
> > The Netherlands
> >
> > Contact:
> > E-Mail: jm.horschig at donders.ru.nl
> > Tel: +31-(0)24-36-68493
> > Web: http://www.ru.nl/donders
> >
> > Visiting address:
> > Trigon, room 2.30
> > Kapittelweg 29
> > NL-6525 EN Nijmegen
> > The Netherlands
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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