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Hi FT-users,<br>
<br>
Sorry for a long email but I hope someone could help with my
question(s) below. Thanks for your patience:<br>
<br>
I am actually interested in both baseline and stim-on periods of the
data collected from an auditory task. <br>
However, since I have not used MNE before I though I'd follow the
tutorial 1st.
<a class="moz-txt-link-freetext" href="http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate">http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate</a><br>
<br>
So I created a timelock variable testTLK that is first bandpassed to
a freq of interest.<br>
<blockquote type="cite"> cfg=[];<br>
cfg.channel = [{'MEG'} badChansList];<br>
<font color="#3333ff">cfg.bpfreq = [1 1].*cond</font>
<br>
cData = ft_preprocessing(cfg,cleanData)<br>
% <br>
cfg.covariance = 'yes'; %'no' or 'yes'
(default = 'no')<br>
<font color="#ff0000"> cfg.covariancewindow = [-inf
0]; %'prestim', 'poststim', 'all' or [begin end] (default =
'all')</font><br>
cfg.keeptrials = 'yes';% 'yes' or 'no', return
individual trials or average (default = 'no')<br>
cfg.removemean = 'yes'; %'no' or 'yes' for
covariance computation (default = 'yes')<br>
cfg.vartrllength = 0; <br>
<br>
testTLK = ft_timelockanalysis(cfg, cData)</blockquote>
<blockquote type="cite">testTLK = <br>
<br>
avg: [233x4069 double]<br>
var: [233x4069 double]<br>
time: [1x4069 double]<br>
dof: [233x4069 double]<br>
label: {233x1 cell}<br>
trial: [96x233x4069 double]<br>
dimord: 'rpt_chan_time'<br>
cov: [96x233x233 double]<br>
cfg: [1x1 struct]</blockquote>
<br>
Then I followed the next steps to estimate MNE source (src) of
testTLK and also requested to keep the filter as I would eventually
like to reconstruct the source signals... (this presumably will work
as described previously
<a class="moz-txt-link-freetext" href="http://mailman.science.ru.nl/pipermail/fieldtrip/2009-December/002500.html">http://mailman.science.ru.nl/pipermail/fieldtrip/2009-December/002500.html</a>)
<br>
<br>
<blockquote type="cite">>> cfg = [];<br>
cfg.method = 'mne';<br>
cfg.grid = fwdmodGRID{sess,2}; %leadfield;<br>
cfg.vol = volm;<br>
cfg.grad=gradInfo(sess,2)<br>
cfg.mne.prewhiten = 'yes';<br>
cfg.mne.lambda = 3;<br>
cfg.mne.scalesourcecov = 'yes';<br>
<br>
cfg.mne.keepfilter = 'yes'; % remember the filter<br>
<br>
src = ft_sourceanalysis(cfg,testTLK);</blockquote>
<blockquote type="cite">>> src<br>
<br>
src = <br>
<br>
dim: [38 48 41]<br>
time: [1x4069 double]<br>
pos: [74784x3 double]<br>
inside: [1x34873 double]<br>
outside: [1x39911 double]<br>
method: 'average'<br>
avg: [1x1 struct]<br>
cfg: [1x1 struct]<br>
<br>
>> src.avg<br>
<br>
ans = <br>
<br>
mom: {74784x1 cell}<br>
pow: [74784x4069 double]<br>
filter: {74784x1 cell}<br>
noisecov: {74784x1 cell}</blockquote>
<br>
Which seems to work in giving me a filter variable within src.avg.<br>
<br>
However, IF I would like to look at the source signals in both
Baseline and StimDuration for comparison<br>
Q1: Should I redefine trials for e.g. BLcond for time [-1 0] and
Stimcond for time [0 2] before the timelock analysis and then
sourceanalysis?<br>
Q2: What would be an appropriate covariance window with regards to
my 2 periods of interest? <br>
e.g. Do I specify <font color="#ff0000">cfg.covariancewindow =
'all' or [begin end]</font> ?<br>
<br>
Eventually, I would hope to be able to follow the example of
computing sources for the 2 conditions for stats to pinpoint to the
source(s) of e.g. maximally elicited power and derive the source
power timeseries.<br>
<blockquote type="cite">% cfg = [];<br>
% cfg.projectmom = 'yes';<br>
% sdFC = ft_sourcedescriptives(cfg,sourceFC);<br>
% sdFIC = ft_sourcedescriptives(cfg, sourceFIC);<br>
%<br>
% sdDIFF = sdFIC;<br>
% sdDIFF.avg.pow = sdFIC.avg.pow - sdFC.avg.pow;<br>
% sdDIFF.tri = sourcespace.tri;<br>
</blockquote>
<br>
<br>
Additionally, following the example to visualize I get an error wrt
to the color specification <br>
Q3: What is a good way to correct this (if variable m also includes
NaN)?<br>
The example<br>
<blockquote type="cite">% bnd.pnt = sourcespace.pnt;<br>
% bnd.tri = sourcespace.tri;<br>
% m=sourceFIC.avg.pow(:,450); % plotting the result at the 450th
time-point that is<br>
% % 500 ms after the zero time-point<br>
% ft_plot_mesh(bnd, 'vertexcolor', m);<br>
</blockquote>
What I used:<br>
<blockquote type="cite">m=nanmean(squeeze(src.avg.pow(:,[1200:3033])),2)<br>
ft_plot_mesh(volm.bnd, 'vertexcolor', m);<br>
</blockquote>
<blockquote type="cite">Error using ft_plot_mesh (line 311)<br>
Unknown color specification for the vertices <br>
</blockquote>
<br>
I'd appreciate if someone could kindly offer some advise to my
questions!<br>
<br>
Many thanks,<br>
May<br>
<br>
<br>
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<p class="MsoNormal"
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<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span class="SpellE"><span
style="font-size:8.0pt;color:#595959;
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mso-style-textfill-fill-colortransforms:"lumm=65000
lumo=35000"">Heng-Ru</span></span><span
style="font-size:8.0pt;color:#595959;mso-themecolor:text1;mso-themetint:166;
mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:text1;
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"lumm=65000
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Tan,
PhD.<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span
style="font-size:8.0pt;color:#595959;mso-themecolor:text1;
mso-themetint:166;mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:
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<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span
style="font-size:8.0pt;color:#595959;mso-themecolor:text1;
mso-themetint:166;mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:
text1;mso-style-textfill-fill-alpha:100.0%;mso-style-textfill-fill-colortransforms:
"lumm=65000
lumo=35000"">Institute of Neuroscience and Psychology
(INP) </span><span
style="font-size:8.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;
color:#595959;mso-themecolor:text1;mso-themetint:166;mso-style-textfill-fill-color:
#595959;mso-style-textfill-fill-themecolor:text1;mso-style-textfill-fill-alpha:
100.0%;mso-style-textfill-fill-colortransforms:"lumm=65000
lumo=35000"">▫
Centre for Cognitive Neuroimaging (<span class="SpellE">CCNi</span>)</span><span
style="font-size:8.0pt;color:#595959;mso-themecolor:text1;mso-themetint:166;
mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:text1;
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style="font-size:8.0pt;mso-bidi-font-family:
Calibri;mso-bidi-theme-font:minor-latin;color:#595959;mso-themecolor:text1;
mso-themetint:166;mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:
text1;mso-style-textfill-fill-alpha:100.0%;mso-style-textfill-fill-colortransforms:
"lumm=65000
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Sciences </span><span
style="font-size:8.0pt;color:#595959;mso-themecolor:text1;
mso-themetint:166;mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:
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"lumm=65000
lumo=35000""><o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span
style="font-size:8.0pt;color:#595959;mso-themecolor:text1;
mso-themetint:166;mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:
text1;mso-style-textfill-fill-alpha:100.0%;mso-style-textfill-fill-colortransforms:
"lumm=65000
lumo=35000"">University of Glasgow </span><span
style="font-size:
8.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;color:#595959;
mso-themecolor:text1;mso-themetint:166;mso-style-textfill-fill-color:#595959;
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mso-style-textfill-fill-colortransforms:"lumm=65000
lumo=35000"">▫ 58 <span class="SpellE">Hillhead</span>
Street, Glasgow G12 8QB</span><span
style="font-size:8.0pt;color:#595959;mso-themecolor:text1;mso-themetint:166;
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mso-style-textfill-fill-alpha:100.0%;mso-style-textfill-fill-colortransforms:
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style="font-size:8.0pt;mso-bidi-font-family:
Calibri;mso-bidi-theme-font:minor-latin;color:#595959;mso-themecolor:text1;
mso-themetint:166;mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:
text1;mso-style-textfill-fill-alpha:100.0%;mso-style-textfill-fill-colortransforms:
"lumm=65000
lumo=35000"">▫ +44 (0)141-330-5090</span><span
style="font-size:8.0pt;color:#595959;mso-themecolor:text1;mso-themetint:166;
mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:text1;
mso-style-textfill-fill-alpha:100.0%;mso-style-textfill-fill-colortransforms:
"lumm=65000
lumo=35000""> </span><span
style="font-size:8.0pt;mso-bidi-font-family:
Calibri;mso-bidi-theme-font:minor-latin;color:#595959;mso-themecolor:text1;
mso-themetint:166;mso-style-textfill-fill-color:#595959;mso-style-textfill-fill-themecolor:
text1;mso-style-textfill-fill-alpha:100.0%;mso-style-textfill-fill-colortransforms:
"lumm=65000
lumo=35000"">▫ <a class="moz-txt-link-abbreviated" href="mailto:Heng-RuMay.Tan@glasgow.ac.uk">Heng-RuMay.Tan@glasgow.ac.uk</a></span><span
style="font-size:8.0pt;color:#595959;mso-themecolor:text1;mso-themetint:166;
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"lumm=65000
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