[FieldTrip] source statistics with ROI yields NaN clusters

Thu Oct 17 12:32:36 CEST 2013

Hi Vitoria,

the change should be from September 24, when we had our last bug binge.
the xgrid, ygrid and zgrid variables should not matter - actually that 
should be deleted from the tutorial. However, what I meant was not that 
you build the grids in MNI space, but interpolate the grid with a 1cm 
or0.8cm resolution to the full MNI template using ft_sourceinterpolate, 
just like you would before plotting. But, I have no clue what has 
changed in the code, so this is just a desperate idea :) I think it 
would be wise to check with JM when he is back, as he is the 
source-guru. Could you open up a new bug for this? Then it might be 
easier for us (i.e. JM) to work on this.

Best,
Jörn

On 10/17/2013 10:30 AM, Vitória Piai wrote:
>
> 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 <mailto:roeysc at gmail.com>>
> > To: FieldTrip discussion list <fieldtrip at science.ru.nl 
> <mailto: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 
> <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto:fieldtrip at donders.ru.nl>
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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-- 
Jörn 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

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