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<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Hi Nathan, <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>thank you very much for
your response! <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Performing source
analysis on data not normalized to the template brain now gives me reasonable
results. I will however, try to figure out, what I was doing wrong with the
normalized data (even though plotting of my virtual grid looked fine there,
too).<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Thanks again!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Nina<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>Von:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> FieldTrip
discussion list [mailto:FIELDTRIP@NIC.SURFNET.NL] <b><span style='font-weight:
bold'>Im Auftrag von </span></b>Nathan Weisz<br>
<b><span style='font-weight:bold'>Gesendet:</span></b> Dienstag, 27. April 2010
15:41<br>
<b><span style='font-weight:bold'>An:</span></b> FIELDTRIP@NIC.SURFNET.NL<br>
<b><span style='font-weight:bold'>Betreff:</span></b> Re: [FIELDTRIP] TFRs on
virtual source data, Neuromag 122</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>hi nina,<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>did you validate the position by plotting them on the individuals MRI?<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>I mean the ones you define in xgrid, ygrid and zgrid.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>when i project my data into source space to do e.g. time-frequencystuff
i do:<o:p></o:p></span></font></p>
</div>
<div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>cfg=[];<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>cfg.vol=vol;<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>cfg.grid.pos=rois; %%here is a difference to your code<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>cfg.grad=data.grad;<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>cfg.channel={'MEG'};<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>grid=prepare_leadfield(cfg);<o:p></o:p></span></font></p>
</div>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>then i continue with the sourceanalysis stuff.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>good luck,<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>n<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>On 27.04.2010, at 14:23, Nina wrote:<o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><br>
<br>
<o:p></o:p></span></font></p>
<div link=blue vlink=purple>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>Hi
all,<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>I
am working on constructing a virtual sensor for my 122 Neuromag MEG data in
order to compute time frequency analysis on this virtual sensor. <u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>The
results I am getting so far are not in line with the sensor level data. On
sensor level I see a very clear gamma response. It is also present on source
level in the frequency domain, using dics, however, the time course of the
source is not as strong and frequency confined on source level. Does anybody
have any ideas on what I might be doing wrong?<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>In
the following, I would like to explain what I have done so far and what my
problems are. I am attaching the script I used in text format.<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial;
font-weight:bold'>About the data set:<u1:p></u1:p></span></font></b><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>It
contains trials of three different conditions. These trials are of variable
lengths (spread evenly over the conditions) and there are not always the same
number of trials in each condition. <u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial;
font-weight:bold'><u1:p> </u1:p></span></font></b><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial;
font-weight:bold'>What I have done so far:<u1:p></u1:p></span></font></b><o:p></o:p></p>
<ol start=1 type=1>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
mso-list:l0 level1 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>based on TFRs on sensor level I
chose each subject’s strongest gamma frequency <u1:p></u1:p></span></font><o:p></o:p></li>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
mso-list:l0 level1 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>for each subject, I took this
frequency (+/- 5 Hz) and calculated spatial filters for stimulation and
baseline periods, averaged over all three conditions using a DICS
beamformer <u1:p></u1:p></span></font><o:p></o:p></li>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
mso-list:l0 level1 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>for each voxel, the ratio of
poststimulus power to prestimulus power was computed</span></font><span
lang=EN-GB> </span><o:p></o:p></li>
<u1:p></u1:p>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
mso-list:l0 level1 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>from that I took the voxel with
maximum power increase and used it as my voxel of interest,</span></font><span
lang=EN-GB> </span><o:p></o:p></li>
<u1:p></u1:p>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
mso-list:l0 level1 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>for this voxel of interest I
calculated a new dipole grid with only one voxel. It is in the same
location as the strongest voxel from step 3.<u1:p></u1:p></span></font><o:p></o:p></li>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
mso-list:l0 level1 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>then I went back to my
functional data and used the FT function ‘timelockanalysis’ to compute the
covariance matrices for all my sensors and trials (keeping single trials),
trying different time windows for covariance computation, but always
calculating power for the whole time period:</span></font><span
lang=EN-GB> </span><o:p></o:p></li>
</ol>
<u1:p></u1:p>
<ol start=6 type=1>
<ol start=1 type=a>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
auto;mso-list:l0 level2 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>pre stimulus [-2 0] (but using
the whole trial for timelockanalysis; time = [-2 3], <u1:p></u1:p></span></font><o:p></o:p></li>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
auto;mso-list:l0 level2 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>post stimulus [0 3] (but using
the whole trial for timelockanalysis; time = [-2 3],</span></font><span
lang=EN-GB> </span><o:p></o:p></li>
<u1:p></u1:p>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
auto;mso-list:l0 level2 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>the whole time period [-2 3],<u1:p></u1:p></span></font><o:p></o:p></li>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
auto;mso-list:l0 level2 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>pre stimulus [-2 0] (using
only that time window for timelockanalysis; time = [-2 0], <u1:p></u1:p></span></font><o:p></o:p></li>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
auto;mso-list:l0 level2 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>post stimulus [0 2] (using
only that time window for timelockanalysis; time = [0 2]<u1:p></u1:p></span></font><o:p></o:p></li>
</ol>
</ol>
<ol start=7 type=1>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
mso-list:l0 level1 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>the covariance matrices were
put into source analysis, again computing spatial filters for the voxel of
interest (using rawtrial = ‘yes’)<u1:p></u1:p></span></font><o:p></o:p></li>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
mso-list:l0 level1 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>NaNs, that were due to
different lengths of trials, in dipole moments resulting from source
analysis were removed<u1:p></u1:p></span></font><o:p></o:p></li>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
mso-list:l0 level1 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>then I put the resulting dipole
moments of the three directions (x,y,z) into a structure that resembles
that of preprocessed data<u1:p></u1:p></span></font><o:p></o:p></li>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
mso-list:l0 level1 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>time frequency representations
of power were calculated using a multitaper approach<u1:p></u1:p></span></font><o:p></o:p></li>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
mso-list:l0 level1 lfo1'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>When looking at the three
directions (x,y,z,) separately in a time frequency plot, this gives me</span></font><span
lang=EN-GB> </span><o:p></o:p></li>
</ol>
<u1:p></u1:p>
<ol start=11 type=1>
<ol start=1 type=a>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
auto;mso-list:l0 level2 lfo2'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>somehow meaningful results for
the covariance window being pre stimulus (5.a), however, they are a lot
weaker than on sensor level.</span></font><span lang=EN-GB> </span><o:p></o:p></li>
<u1:p></u1:p>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
auto;mso-list:l0 level2 lfo2'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>no meaningful results for the
covariance window being post stimulus (5.b) or the whole time period (5.c)<u1:p></u1:p></span></font><o:p></o:p></li>
</ol>
</ol>
<ol start=12 type=1>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
mso-list:l0 level1 lfo2'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>for 5. d/e relative changes to
baseline were calculated for each of the trials <u1:p></u1:p></span></font><o:p></o:p></li>
</ol>
<ol start=12 type=1>
<ol start=1 type=a>
<li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
auto;mso-list:l0 level2 lfo3'><font size=2 face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial'>this gives me somehow meaningful
results, but very weak and not constrained to the before found frequency
ranges<u1:p></u1:p></span></font><o:p></o:p></li>
</ol>
</ol>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>Does
anybody have experience with this kind of analysis? Do you have any suggestions
about which step might be causing these troubles? <u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>Thank
you all in advance for any help!<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 face=Arial><span lang=EN-GB style='font-size:10.0pt;font-family:Arial'>Nina<u1:p></u1:p></span></font><o:p></o:p></p>
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<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>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.<o:p></o:p></span></font></p>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'><a
href="http://listserv.surfnet.nl/archives/fieldtrip.html">http://listserv.surfnet.nl/archives/fieldtrip.html</a><o:p></o:p></span></font></p>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'><a
href="http://www.ru.nl/fcdonders/fieldtrip/">http://www.ru.nl/fcdonders/fieldtrip/</a><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><virtualsensor.txt><o:p></o:p></span></font></p>
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12.0pt'><o:p> </o:p></span></font></p>
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<p>----------------------------------</p>
<p>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.</p>
<p> http://listserv.surfnet.nl/archives/fieldtrip.html</p>
<p> http://www.ru.nl/fcdonders/fieldtrip/</p>
<p>----------------------------------</p>
<p>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.</p>
<p> http://listserv.surfnet.nl/archives/fieldtrip.html</p>
<p> http://www.ru.nl/fcdonders/fieldtrip/</p>