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Actually I don't think so.<br><br>I first computed the sourcestatistics.<br>Then I interpolated the Stats and visualized them with sourceplot and cfg.interactive = yes.<br><br>Frederic<br><br><br><br><br><hr id="stopSpelling">Date: Fri, 4 Dec 2009 14:58:23 +0100<br>From: ingrid.nieuwenhuis@FCDONDERS.RU.NL<br>Subject: Re: [FIELDTRIP] interpolated source activity values = NaN<br>To: FIELDTRIP@NIC.SURFNET.NL<br><br>
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<p class="ecxMsoNormal"><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;">Dear Frederic,</span></font></p>
<p class="ecxMsoNormal"><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<p class="ecxMsoNormal"><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;">Could it be that you wrote down the
indices of the voxels before interpolating? Since the voxels before
interpolating do not match anymore after interpolating onto the template_mri.</span></font></p>
<p class="ecxMsoNormal"><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<p class="ecxMsoNormal"><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;">Best,</span></font></p>
<p class="ecxMsoNormal"><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;">Ingrid</span></font></p>
<p class="ecxMsoNormal"><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
<p class="ecxMsoNormal"><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font></p>
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<p class="ecxMsoNormal"><b><font face="Tahoma" size="2"><span style="font-size: 10pt; font-family: Tahoma; font-weight: bold;">From:</span></font></b><font face="Tahoma" size="2"><span style="font-size: 10pt; font-family: Tahoma;"> FieldTrip
discussion list [mailto:FIELDTRIP@NIC.SURFNET.NL] <b><span style="font-weight: bold;">On Behalf Of </span></b>Frederic Roux<br>
<b><span style="font-weight: bold;">Sent:</span></b> Friday, December 04, 2009
2:51 PM<br>
<b><span style="font-weight: bold;">To:</span></b> FIELDTRIP@NIC.SURFNET.NL<br>
<b><span style="font-weight: bold;">Subject:</span></b> Re: [FIELDTRIP]
interpolated source activity values = NaN</span></font></p>
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<p class="ecxMsoNormal" style="margin-bottom: 12pt;"><font face="Verdana" size="2"><span style="font-size: 10pt; font-family: Verdana;">Hi Ingrid,<br>
<br>
thanks for the quick reply. I will try your suggestion but I am pretty much
sure that the values I want to look at are inside the brain.<br>
<br>
My approach is the following:<br>
<br>
I want to indentify the voxels that show significant activation.<br>
So first I visualized my data with sourceplot and cfg.interactive = 'yes' and
then I write down the indices of the voxels onto which I click.<br>
<br>
When I feed these indices into SourceInterpolatedStats.stat([x y z]) this
returns me NaNs, even tough the voxel was clearly located inside the brain.<br>
<br>
Do you have any idea of why this happens?<br>
<br>
Frederic</span></font></p>
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<p class="ecxMsoNormal" style="margin-bottom: 12pt;"><font face="Verdana" size="2"><span style="font-size: 10pt; font-family: Verdana;">Date: Fri, 4 Dec 2009 13:21:17
+0100<br>
From: ingrid.nieuwenhuis@FCDONDERS.RU.NL<br>
Subject: Re: [FIELDTRIP] interpolated source activity values = NaN<br>
To: FIELDTRIP@NIC.SURFNET.NL</span></font></p>
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<p class="ecxMsoNormal"><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;">Hi Frederic,</span></font><font face="Verdana" size="2"><span style="font-size: 10pt; font-family: Verdana;"></span></font></p>
<p class="ecxMsoNormal"><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;"> </span></font><font face="Verdana" size="2"><span style="font-size: 10pt; font-family: Verdana;"></span></font></p>
<p class="ecxMsoNormal"><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;">Probably the NaN’s
are the voxels outside the brain. The source estimate is only performed for
voxels inside the brain, the voxels outside are put to NaN.
In the field “inside” it is coded which voxels lay inside the brain. Try:</span></font><font face="Verdana" size="2"><span style="font-size: 10pt; font-family: Verdana;"></span></font></p>
<p class="ecxMsoNormal"><font face="Verdana" size="2"><span style="font-size: 10pt; font-family: Verdana;">SourceInterpolatedStats.stat(SourceInterpolatedStats.inside)</span></font></p>
<p class="ecxMsoNormal"><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;">This should give you the non-NaN values.</span></font><font face="Verdana" size="2"><span style="font-size: 10pt; font-family: Verdana;"></span></font></p>
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<p class="ecxMsoNormal"><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;">Hope this helps,</span></font><font face="Verdana" size="2"><span style="font-size: 10pt; font-family: Verdana;"></span></font></p>
<p class="ecxMsoNormal"><font color="navy" face="Arial" size="2"><span style="font-size: 10pt; font-family: Arial; color: navy;">Ingrid</span></font><font face="Verdana" size="2"><span style="font-size: 10pt; font-family: Verdana;"></span></font></p>
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<p class="ecxMsoNormal"><b><font face="Tahoma" size="2"><span style="font-size: 10pt; font-family: Tahoma; font-weight: bold;">From:</span></font></b><font face="Tahoma" size="2"><span style="font-size: 10pt; font-family: Tahoma;"> FieldTrip
discussion list [mailto:FIELDTRIP@NIC.SURFNET.NL] <b><span style="font-weight: bold;">On Behalf Of </span></b>Frederic Roux<br>
<b><span style="font-weight: bold;">Sent:</span></b> Friday, December 04, 2009
12:51 PM<br>
<b><span style="font-weight: bold;">To:</span></b> FIELDTRIP@NIC.SURFNET.NL<br>
<b><span style="font-weight: bold;">Subject:</span></b> [FIELDTRIP] interpolated
source activity values = NaN</span></font><font face="Verdana" size="2"><span style="font-size: 10pt; font-family: Verdana;"></span></font></p>
</div>
<p class="ecxMsoNormal"><font face="Times New Roman" size="3"><span style="font-size: 12pt;"> </span></font><font face="Verdana" size="2"><span style="font-size: 10pt; font-family: Verdana;"></span></font></p>
<p class="ecxMsoNormal" style="margin-bottom: 12pt;"><font face="Verdana" size="2"><span style="font-size: 10pt; font-family: Verdana;">Hi everyone,<br>
<br>
I would like to use the values that correspond to the interpolated statistics
at source level. <br>
The problem is that most of these values are NaNs, even tough I can visualize
them with sourceplot.<br>
<br>
Here are the steps I am doing to compute these values:<br>
<br>
[signal1] = sourcegrandaverage(cfg,data);<br>
[signal2] = sourcegrandaverage(cfg,data);<br>
<br>
[Stats] = sourcestatistics(cfg,signal1,signal2);%the statistics used here is
depsamplesT using fdr and clusterstatistics = maxsum<br>
[SourceInterpolatedSats] = sourceinterpolate(cfg,Stats,template_mri);<br>
<br>
This yields:<br>
<br>
SourceInterpolatedSats =<br>
<br>
inside: [91x109x91 logical]<br>
stat: [91x109x91 double]<br>
dim: [91 109 91]<br>
transform: [4x4 double]<br>
anatomy: [91x109x91 double]<br>
cfg: [1x1 struct]<br>
<br>
But when I try :<br>
<br>
SourceInterpolatedStats.stat([20 45 68]) = NaN.<br>
And this holds true for almost any index.<br>
<br>
Does anyone know if it's possible to access these values?<br>
<br>
Frederic</span></font></p>
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The aim of this list is to facilitate the discussion between users of the
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The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis.<BR>
http://listserv.surfnet.nl/archives/fieldtrip.html<BR>
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The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis.<BR>
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