<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div><div style="text-align: left;direction: ltr; "><span style="-webkit-text-size-adjust: auto;">Hi Vitoria and everyone else,</span></div><div style="text-align: left;direction: ltr; "><span style="-webkit-text-size-adjust: auto;"><br></span></div><div style="text-align: left;direction: ltr; "><span style="-webkit-text-size-adjust: auto;">I agree with </span><span style="-webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: auto; ">Jörn (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.</span></div><div style="text-align: left;direction: ltr; "><span style="-webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: auto; "><br></span></div><div style="text-align: left;direction: ltr; "><span style="-webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: auto; ">A possible solution could be having the atlas we are using available to that function, and translating the B side to the voxel space.</span></div><div style="text-align: left;direction: ltr; "><span style="-webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: auto; "><br></span></div><div style="text-align: left;direction: ltr; "><span style="-webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: auto; ">By the way, are you using an MNI grid per subject?</span></div><div style="text-align: left;direction: ltr; "><span style="-webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: auto; "><br></span></div><div style="text-align: left;direction: ltr; "><span style="-webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: auto;">Best,</span></div><div style="text-align: left;direction: ltr; "><span style="-webkit-tap-highlight-color: rgba(26, 26, 26, 0.292969); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); -webkit-text-size-adjust: auto;">roey</span></div><br><div style="-webkit-text-size-adjust: auto; text-align: left; direction: ltr; "><br></div></div><div style="-webkit-text-size-adjust: auto; "><br>ב-16 באוק 2013, בשעה 17:07, "Jörn M. Horschig" <<a href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a>> כתב/ה:<br><br></div><blockquote type="cite" style="-webkit-text-size-adjust: auto; "><div>
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<div class="moz-cite-prefix">Hi Vitoria,<br>
<br>
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 ;)<br>
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? <br>
<br>
Best,<br>
Jörn<br>
<br>
<br>
On 10/16/2013 11:19 AM, Vitória Magalhães Piai wrote:<br>
</div>
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Dear all, <br>
<br>
I'm trying to run ft_sourcestatistics with a specified ROI. It's
data (MNEs) averaged over time.<br>
<br>
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.<br>
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. <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,
statobs,'issource',issource);<br>
Error in ==> statistics_wrapper at 298<br>
[stat, cfg] = statmethod(cfg, dat, design,
'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
stat.posclusters/negclusters is only NaN. This is regardless of
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
days, so <i>any</i> help would be highly appreciated, even if it
is to suggest another way to do the stats!<br>
<br>
Thanks a lot, Vitória<br>
<br>
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<br>
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<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>
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