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Dear Tara, </div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Thank you very much for your suggestion, but I already tried to run the Cluster-based on raw power in the baseline time-interval and no significant cluster has been detected.</div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
So, it seems that this difference between raw power and baseline-corrected one can't be explained by existing differences in the baseline period.</div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Hope that you have other suggestions, </div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Thank you in advance, </div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Eleonora</div>
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<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> fieldtrip <fieldtrip-bounces@science.ru.nl> on behalf of fieldtrip-request@science.ru.nl <fieldtrip-request@science.ru.nl><br>
<b>Sent:</b> Tuesday, October 8, 2019 12:00 PM<br>
<b>To:</b> fieldtrip@science.ru.nl <fieldtrip@science.ru.nl><br>
<b>Subject:</b> fieldtrip Digest, Vol 107, Issue 4</font>
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<div class="PlainText">Send fieldtrip mailing list submissions to<br>
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To subscribe or unsubscribe via the World Wide Web, visit<br>
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Today's Topics:<br>
<br>
1. Re: Small Issues with the 15684 Mesh Creation Procedure<br>
(Schoffelen, J.M. (Jan Mathijs))<br>
2. baseline correction - Cluster Based Permutation Test<br>
(eleonora parrotta)<br>
3. Re: baseline correction - Cluster Based Permutation Test<br>
(Tara van Viegen)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 7 Oct 2019 12:33:27 +0000<br>
From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen@donders.ru.nl><br>
To: FieldTrip discussion list <fieldtrip@science.ru.nl><br>
Subject: Re: [FieldTrip] Small Issues with the 15684 Mesh Creation<br>
Procedure<br>
Message-ID: <C7A4D2E1-171C-4D79-A398-99EF2126A762@donders.ru.nl><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Paolo,<br>
<br>
@1: I have not encountered the issue you describe. Probably it is the consequence of the fact that the anatomical images you use are different as compared to ours, e.g. in terms of voxel sizes, field-of-view, acquisition sequence. I am no expert in mri_convert,
but this function has some options that might tweak its behavior such that it does justice to your anatomical images.<br>
<br>
@2: If you run the post processing script (which relies on hcp-workbench) the meshes will be surface-registered to a template, which allows for direct vertex-wise comparison across subjects (as well as across hemispheres).<br>
<br>
Best,<br>
Jan-Mathijs<br>
<br>
<br>
<br>
On 2 Oct 2019, at 11:35, Paolo Belardinelli <paolo.belardinelli@gmail.com<mailto:paolo.belardinelli@gmail.com>> wrote:<br>
<br>
Dear all,<br>
I would first like to thank Jan-Mathijs for the massive work on the mesh sourcemodel.<br>
I encountered a couple of minor issues while implementing the whole process:<br>
<br>
1. In some subjects, after saving the .mgz file with Fieldtrip (including acpc coordinates and reference point), the image is slightly shifted towards the superior side of the frame by mriconvert (mri_convert -c -oc 0 0 0 $SUBJECTNAME.mgz orig.mgz). This implies
that the upper part of the brain is being chopped and the further segmentation process with recon -all makes no sense anymore. Has anyone the same issue?<br>
<br>
2. As far as I understand, an average, atlas-mapped mesh where to visualize pooled results is not generated. What would be a straightforward way of visualizing group results in standard coordinates?<br>
<br>
Best wishes,<br>
<br>
Paolo<br>
<br>
--<br>
--<br>
Paolo Belardinelli, PhD<br>
Neurology Department<br>
University Hospital Tuebingen<br>
Eberhard Karls University Tuebingen<br>
Hoppe-Seyler Str. 3<br>
D-72076 Tuebingen<br>
Tel: +49 7071 / 29 80478<br>
<br>
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<br>
Message: 2<br>
Date: Mon, 7 Oct 2019 16:12:30 +0000<br>
From: eleonora parrotta <eleonora_p@hotmail.it><br>
To: "fieldtrip@science.ru.nl" <fieldtrip@science.ru.nl><br>
Subject: [FieldTrip] baseline correction - Cluster Based Permutation<br>
Test<br>
Message-ID:<br>
<DB8PR10MB31155EC46EAD26EFB120F7A18D9B0@DB8PR10MB3115.EURPRD10.PROD.OUTLOOK.COM><br>
<br>
Content-Type: text/plain; charset="windows-1252"<br>
<br>
Dear Fieldtrippers,<br>
<br>
I am performing analysis of EEG data. I have two conditions of interest: A and B, and I have performed spectral decomposition with the wavelet method to obtain the power (frequencies from 1 to 50 Hz).<br>
<br>
I performed a cluster-based permutation test to assess whether there are significant power differences between the two conditions of interest in the time-interval from the onset of the stimulus to 1 sec after:<br>
<br>
%% clusterbased analysis<br>
<br>
cfg = [];<br>
<br>
cfg.latency = [0 1]; % Time of Interest<br>
<br>
cfg.frequency = [8 12]; % Frequency of interest<br>
<br>
cfg.channel = {'PO3', 'P3', 'O1', 'P7','O2','P8','PO4','P4'};<br>
<br>
cfg.neighbours = neighbours;<br>
<br>
cfg.avgoverfreq = 'yes';<br>
<br>
cfg.avgovertime = 'no';<br>
<br>
cfg.avgoverchannel = 'no';<br>
<br>
cfg.method = 'montecarlo';<br>
<br>
cfg.statistic = 'ft_statfun_depsamplesT';<br>
<br>
subj = 18;<br>
<br>
design = zeros(2,2*subj);<br>
<br>
for i = 1:subj<br>
<br>
design(1,i) = i;<br>
<br>
end<br>
<br>
for i = 1:subj<br>
<br>
design(1,subj+i) = i;<br>
<br>
end<br>
<br>
design(2,1:subj)= 1;design(2,subj+1:2*subj) = 2;<br>
<br>
cfg.design = design;<br>
<br>
cfg.uvar = 1;<br>
<br>
cfg.ivar = 2;<br>
<br>
cfg.correctm = 'cluster';<br>
<br>
cfg.clusteralpha = 0.05;<br>
<br>
cfg.clusterstatistic = 'maxsum';<br>
<br>
cfg.minnbchan = 2;% specifies with which sensors other sensors can form clusters<br>
<br>
cfg.tail = 0;<br>
<br>
cfg.clustertail = 0;<br>
<br>
cfg.alpha = 0.05;<br>
<br>
cfg.numrandomization = 1000;<br>
<br>
[alpha] = ft_freqstatistics(cfg, avg_pred, avg_ran);<br>
<br>
<br>
<br>
When I perform the cluster-based analysis on raw power I obtain more than one negative cluster, with highly significant differences between my two condition (p=0.01). The problem is that when I run the cluster-based analysis on baseline-corrected power the
analysis is not even able to find any cluster of electrodes that behave differently in one condition compared to the other one (no matter which kind of baseline I applied, I tried with both ‘absolute’ and ‘relchange’ and even different time-window).<br>
<br>
I am aware of the potential loss of power that can occur when we use baseline-correction (<a href="http://datacolada.org/39">http://datacolada.org/39</a>)<br>
<br>
At the same time I am not sure how correct is to perform stats on non-baseline corrected power, as without applying this procedure drifts and offsets potentially present in the signal could affect the statistical test, executed on two non-normalized datasets.<br>
<br>
I was wondering whether I am not aware of potential ways to specify that a baseline-correction has been applied to the data, or if there is a correct way of doing it.<br>
<br>
So far I couldn’t find any reference that explains it clearly, but if anyone has an explanation I would really appreciate.<br>
<br>
<br>
<br>
Thanks in advance,<br>
<br>
<br>
<br>
Eleonora<br>
<br>
<br>
<br>
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------------------------------<br>
<br>
Message: 3<br>
Date: Mon, 7 Oct 2019 13:49:04 -0400<br>
From: Tara van Viegen <taravanviegen@gmail.com><br>
To: FieldTrip discussion list <fieldtrip@science.ru.nl><br>
Subject: Re: [FieldTrip] baseline correction - Cluster Based<br>
Permutation Test<br>
Message-ID:<br>
<CAFBE+2n0yaCFpxijCN7LrCtStxmKaKUv8gEZ5v-X3iGTfGCb6g@mail.gmail.com><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Eleonora,<br>
<br>
A likely explanation of what you describe is that there are baseline<br>
differences between your conditions of interest. You could check this by<br>
running the statistics you used previously on the raw power in the time<br>
window that you select as a baseline (e.g. cfg.latency = [-0.5 -0.1];<br>
cfg.avgovertime = 'yes';). The difference you are observing between your<br>
conditions are then explained by differences that already exist in the<br>
baseline. If you apply a baseline correction you get rid of this effect.<br>
<br>
Best,<br>
Tara van Viegen<br>
Senior-RA (aspiring post-doc)<br>
Neuroscience of Attention & Perception Lab<br>
Princeton University<br>
tviegen@princeton.edu<br>
<br>
On Mon, Oct 7, 2019 at 12:34 PM eleonora parrotta <eleonora_p@hotmail.it><br>
wrote:<br>
<br>
> Dear Fieldtrippers,<br>
><br>
> I am performing analysis of EEG data. I have two conditions of interest: A<br>
> and B, and I have performed spectral decomposition with the wavelet method<br>
> to obtain the power (frequencies from 1 to 50 Hz).<br>
><br>
> I performed a cluster-based permutation test to assess whether there are<br>
> significant power differences between the two conditions of interest in the<br>
> time-interval from the onset of the stimulus to 1 sec after:<br>
><br>
> %% clusterbased analysis<br>
><br>
> cfg = [];<br>
><br>
> cfg.latency = [0 1]; % Time of Interest<br>
><br>
> cfg.frequency = [8 12]; % Frequency of interest<br>
><br>
> cfg.channel = {'PO3', 'P3', 'O1', 'P7','O2','P8','PO4','P4'};<br>
><br>
> cfg.neighbours = neighbours;<br>
><br>
> cfg.avgoverfreq = 'yes';<br>
><br>
> cfg.avgovertime = 'no';<br>
><br>
> cfg.avgoverchannel = 'no';<br>
><br>
> cfg.method = 'montecarlo';<br>
><br>
> cfg.statistic = 'ft_statfun_depsamplesT';<br>
><br>
> subj = 18;<br>
><br>
> design = zeros(2,2*subj);<br>
><br>
> for i = 1:subj<br>
><br>
> design(1,i) = i;<br>
><br>
> end<br>
><br>
> for i = 1:subj<br>
><br>
> design(1,subj+i) = i;<br>
><br>
> end<br>
><br>
> design(2,1:subj)= 1;design(2,subj+1:2*subj) = 2;<br>
><br>
> cfg.design = design;<br>
><br>
> cfg.uvar = 1;<br>
><br>
> cfg.ivar = 2;<br>
><br>
> cfg.correctm = 'cluster';<br>
><br>
> cfg.clusteralpha = 0.05;<br>
><br>
> cfg.clusterstatistic = 'maxsum';<br>
><br>
> cfg.minnbchan = 2;% specifies with which sensors other sensors can<br>
> form clusters<br>
><br>
> cfg.tail = 0;<br>
><br>
> cfg.clustertail = 0;<br>
><br>
> cfg.alpha = 0.05;<br>
><br>
> cfg.numrandomization = 1000;<br>
><br>
> [alpha] = ft_freqstatistics(cfg, avg_pred, avg_ran);<br>
><br>
><br>
><br>
> When I perform the cluster-based analysis on raw power I obtain more than<br>
> one negative cluster, with highly significant differences between my two<br>
> condition (p=0.01). The problem is that when I run the cluster-based<br>
> analysis on baseline-corrected power the analysis is not even able to find<br>
> any cluster of electrodes that behave differently in one condition compared<br>
> to the other one (no matter which kind of baseline I applied, I tried with<br>
> both ‘absolute’ and ‘relchange’ and even different time-window).<br>
><br>
> I am aware of the potential loss of power that can occur when we use<br>
> baseline-correction (<a href="http://datacolada.org/39">http://datacolada.org/39</a>)<br>
><br>
> At the same time I am not sure how correct is to perform stats on<br>
> non-baseline corrected power, as without applying this procedure drifts and<br>
> offsets potentially present in the signal could affect the statistical<br>
> test, executed on two non-normalized datasets.<br>
><br>
> I was wondering whether I am not aware of potential ways to specify that a<br>
> baseline-correction has been applied to the data, or if there is a correct<br>
> way of doing it.<br>
><br>
> So far I couldn’t find any reference that explains it clearly, but if anyone has an explanation I would really appreciate.<br>
><br>
><br>
><br>
> Thanks in advance,<br>
><br>
><br>
><br>
> Eleonora<br>
><br>
><br>
><br>
> _______________________________________________<br>
> fieldtrip mailing list<br>
> <a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
> <a href="https://doi.org/10.1371/journal.pcbi.1002202">https://doi.org/10.1371/journal.pcbi.1002202</a><br>
><br>
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End of fieldtrip Digest, Vol 107, Issue 4<br>
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