<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<div class="moz-cite-prefix">Hi Vitoria,<br>
<br>
the change should be from September 24, when we had our last bug
binge.<br>
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.<br>
<br>
Best,<br>
Jörn<br>
<br>
<br>
On 10/17/2013 10:30 AM, Vitória Piai wrote:<br>
</div>
<blockquote
cite="mid:CACtmOgK3kN4=3XWPmVOcGMcDKOtQjJ-3utbJH=yiSeXF98UBWg@mail.gmail.com"
type="cite">
<p>Hi Roey and Joern, </p>
<p>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: <br>
"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." <br>
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?<br>
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 ;) <br>
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.</p>
<p>Roey, yes, I'm using an MNI grid per subject (similar to the
tutorial: <a moz-do-not-send="true"
href="http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space">http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space</a>
> Make the individual subjects' grid).</p>
<p>Cheers, Vitoria</p>
<p>> ------------------------------<br>
> <br>
> Message: 3<br>
> Date: Wed, 16 Oct 2013 20:10:20 +0300<br>
> From: Roey <<a moz-do-not-send="true"
href="mailto:roeysc@gmail.com">roeysc@gmail.com</a>><br>
> To: FieldTrip discussion list <<a moz-do-not-send="true"
href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
> Subject: Re: [FieldTrip] source statistics with ROI yields
NaN<br>
> clusters<br>
> Message-ID: <<a moz-do-not-send="true"
href="mailto:FF996E6D-BAEF-458D-BB41-B9CF1FC5B1DA@gmail.com">FF996E6D-BAEF-458D-BB41-B9CF1FC5B1DA@gmail.com</a>><br>
> Content-Type: text/plain; charset="utf-8"<br>
> <br>
> Hi Vitoria and everyone else,<br>
> <br>
> I agree with J?rn (thank you!) , indeed it seems this is
the same<br>
> problem. Hopefully I'll get back to it next week and maybe
figure it<br>
> out. Right now it seems like the A side consists of all the<br>
> inside-voxels, whereas the B side consists of the different
ROIs, and<br>
> hence the mismatch.<br>
> <br>
> A possible solution could be having the atlas we are using
available<br>
> to that function, and translating the B side to the voxel
space.<br>
> <br>
> By the way, are you using an MNI grid per subject?<br>
> <br>
> Best,<br>
> roey<br>
> <br>
> <br>
> <br>
> ?-16 ???? 2013, ???? 17:07, "J?rn M. Horschig"<br>
> <<a moz-do-not-send="true"
href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a>>
???/?:<br>
> <br>
> > Hi Vitoria,<br>
> ><br>
> > I guess that is the same error that Roey Schurr
described a few days<br>
> > back. There were some changes recently in the atlas
lookup function<br>
> > (we replaced one function and made another more
general). Apparently<br>
> > that broke some things, or you two just happen to do
this as the<br>
> > first ever ;)<br>
> > The only thing I can think of is that you might need
to interpolate<br>
> > to the MNI template so that the dimensions are matched
between the<br>
> > atlas and your source structures. Could you give that
a try and let<br>
> > us know whether that helps?<br>
> ><br>
> > Best,<br>
> > J?rn<br>
> ><br>
> ><br>
> > On 10/16/2013 11:19 AM, Vit?ria Magalh?es Piai wrote:<br>
> >> Dear all,<br>
> >><br>
> >> I'm trying to run ft_sourcestatistics with a
specified ROI. It's<br>
> >> data (MNEs) averaged over time.<br>
> >><br>
> >> If I run ft_sourcestatistics without an ROI, I get
a cluster with<br>
> >> prob = .178. It looks like this (figure attached),
where I masked<br>
> >> using the t-values.<br>
> >> Since I'm dealing with an N400-like component,
I've got good<br>
> >> reasons to expect the effect to be localised
(mainly) to left<br>
> >> temporal areas.<br>
> >><br>
> >> So I tried adding this to my cfg:<br>
> >><br>
> >> cfgst.atlas = 'aal\ROI_MNI_V4.nii';<br>
> >> cfgst.roi = {'Temporal_Mid_L' 'Temporal_Sup_L'
'Temporal_Inf_L' };<br>
> >> cfgst.avgoverroi = 'yes';<br>
> >> cfgst.hemisphere = 'left';<br>
> >> cfgst.inputcoord = 'mni' ;<br>
> >> stat = ft_sourcestatistics(cfgst, iRel{:},
iIde{:});<br>
> >><br>
> >> If cfgst.avgoverroi == 'yes'; I get the following
error:<br>
> >><br>
> >> ??? In an assignment A(:) = B, the number of
elements in A and B<br>
> >> must be the same.<br>
> >> Error in ==> clusterstat at 187<br>
> >> tmp(cfg.inside) = postailobs;<br>
> >> Error in ==> ft_statistics_montecarlo at 326<br>
> >> [stat, cfg] = clusterstat(cfg, statrand,<br>
> >> statobs,'issource',issource);<br>
> >> Error in ==> statistics_wrapper at 298<br>
> >> [stat, cfg] = statmethod(cfg, dat, design,<br>
> >> 'issource',issource);<br>
> >> Error in ==> ft_sourcestatistics at 107<br>
> >> [stat, cfg] = statistics_wrapper(cfg,
varargin{:});<br>
> >><br>
> >> If cfgst.avgoverroi == 'no';<br>
> >> ft outputs "found positive clusters in observed
data" and<br>
> >> stat.posclusters/negclusters is only NaN. This is
regardless of<br>
> >> whether cfgst.roi is one label or a cell array.<br>
> >><br>
> >> Does anyone know what I'm doing wrong?<br>
> >> I've been completely stuck on source statistics
for these MNEs for<br>
> >> days, so any help would be highly appreciated,
even if it is to<br>
> >> suggest another way to do the stats!<br>
> >><br>
> >> Thanks a lot, Vit?ria<br>
> >><br>
> >><br>
> >> _______________________________________________<br>
> >> fieldtrip mailing list<br>
> >> <a moz-do-not-send="true"
href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
> >> <a moz-do-not-send="true"
href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
> ><br>
> ><br>
> > --<br>
> > J?rn M. Horschig<br>
> > PhD Student<br>
> > Donders Institute for Brain, Cognition and Behaviour<br>
> > Centre for Cognitive Neuroimaging<br>
> > Radboud University Nijmegen<br>
> > Neuronal Oscillations Group<br>
> > FieldTrip Development Team<br>
> ><br>
> > P.O. Box 9101<br>
> > NL-6500 HB Nijmegen<br>
> > The Netherlands<br>
> ><br>
> > Contact:<br>
> > E-Mail: <a moz-do-not-send="true"
href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a><br>
> > Tel: +31-(0)24-36-68493<br>
> > Web: <a moz-do-not-send="true"
href="http://www.ru.nl/donders">http://www.ru.nl/donders</a><br>
> ><br>
> > Visiting address:<br>
> > Trigon, room 2.30<br>
> > Kapittelweg 29<br>
> > NL-6525 EN Nijmegen<br>
> > The Netherlands<br>
> > _______________________________________________<br>
> > fieldtrip mailing list<br>
> > <a moz-do-not-send="true"
href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
> > <a moz-do-not-send="true"
href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
> -------------- next part --------------<br>
> An HTML attachment was scrubbed...<br>
> URL:<br>
> <<a moz-do-not-send="true"
href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20131016/239e9cf4/attachment.html">http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20131016/239e9cf4/attachment.html</a>><br>
> <br>
> ------------------------------<br>
> <br>
> _______________________________________________<br>
> fieldtrip mailing list<br>
> <a moz-do-not-send="true"
href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
> <a moz-do-not-send="true"
href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
> <br>
> End of fieldtrip Digest, Vol 35, Issue 29<br>
> *****************************************<br>
</p>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
fieldtrip mailing list
<a class="moz-txt-link-abbreviated" href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>
<a class="moz-txt-link-freetext" href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></pre>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
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: <a class="moz-txt-link-abbreviated" href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a>
Tel: +31-(0)24-36-68493
Web: <a class="moz-txt-link-freetext" href="http://www.ru.nl/donders">http://www.ru.nl/donders</a>
Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands</pre>
</body>
</html>