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<p class=MsoNormal>Hi Eric,<o:p></o:p></p>
<p class=MsoNormal>Thank you very much for the advice.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo3'><![if !supportLists]><span
style='mso-list:Ignore'>1)<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]>With regard to our frequency domain analysis, I’ve
already used FFT to look at general trends in the sample and delay periods but
am interested in plotting the evolution of those oscillations over trial time.
I believe that the cluster analysis and MonteCarlo simulation are the best
method to adopt for quantifying difference between conditions, but please do
correct me if you have other suggestions.<o:p></o:p></p>
<p class=MsoListParagraph><o:p> </o:p></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo3'><![if !supportLists]><span
style='mso-list:Ignore'>2)<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]>Another question is about the edge artifact of using
multitapers at ultralow frequencies on relatively short (57s) data
segments. Are multitapers a good approach, and if so could padding help
with the edge artifact? <o:p></o:p></p>
<p class=MsoListParagraph><o:p> </o:p></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo3'><![if !supportLists]><span
style='mso-list:Ignore'>3)<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]>On a separate note, do you have any functions available/coming
for computing spike-field coherence? Thank you again.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Best,<o:p></o:p></p>
<p class=MsoNormal>Allen<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<p class=MsoNormal><span style='font-size:10.5pt;font-family:Consolas'>__________________________________________________________________________________</span><o:p></o:p></p>
<p class=MsoNormal>Allen Ardestani Email: <a href="mailto:aardesta@ucla.edu"><span
style='color:blue'>aardesta@ucla.edu</span></a><o:p></o:p></p>
<p class=MsoNormal>Phone: (310) 825-5528<o:p></o:p></p>
<p class=MsoNormal>Medical Scientist Training Program<o:p></o:p></p>
<p class=MsoNormal>David Geffen School of Medicine at UCLA<o:p></o:p></p>
<p class=MsoNormal>Semel Institute for Neuroscience and Human Behavior<o:p></o:p></p>
<p class=MsoNormal>760 Westwood Plaza<o:p></o:p></p>
<p class=MsoNormal>Los Angeles, CA 90095-1759<o:p></o:p></p>
<p class=MsoNormal>USA<o:p></o:p></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
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<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> FieldTrip
discussion list [mailto:FIELDTRIP@NIC.SURFNET.NL] <b>On Behalf Of </b>Eric
Maris<br>
<b>Sent:</b> Thursday, April 01, 2010 1:51 PM<br>
<b>To:</b> FIELDTRIP@NIC.SURFNET.NL<br>
<b>Subject:</b> Re: [FIELDTRIP] New FieldTrip User Questions<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'>Hi
Allen,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal style='margin-left:35.4pt'>I just now came across the
FieldTrip toolbox and have a few questions – I apologize in advance if I am
misusing this discussion forum or if my questions are too obvious. I am
working with a very large dataset of simultaneous LFP, unit, and NIRS signal
from macaques for the purpose of examining time and frequency dynamics of the
signals in various cognitive conditions. I would like to implement the
clustering/bootstrapping methodology outlined in [Journal of Neuroscience Methods
164 (2007) 177–190] to identify significant changes in synchronization and
phase-locking. <o:p></o:p></p>
<p class=MsoNormal style='margin-left:35.4pt'><o:p> </o:p></p>
<p class=MsoNormal style='margin-left:35.4pt'>The specific data in question are
LFPs recorded while the monkeys perform a working-memory task, which consists
of a 2s visual sample, 20s delay, and subsequent choice period. A 20s
baseline precedes the sample (t=0), which is time-locked to the animal’s
foveation on the visual sample. TF plots are computed using Morlet
wavelets for each trial, averaged across trials, and then normalized with
respect to the average baseline. The first question I’d like to address
is: what time-frequency regions exhibit significant difference between Correct
(left plot) and Incorrect (right plot) trials. <o:p></o:p></p>
<p class=MsoNormal style='margin-left:35.4pt'><o:p> </o:p></p>
<p class=MsoNormal style='margin-left:35.4pt'><img border=0 width=352
height=264 id="Picture_x005f_x0020_2" src="cid:image001.jpg@01CADD59.3F08A740"
alt="cid:image002.jpg@01CAA0E0.B7CEC3E0"> <img border=0 width=352
height=264 id="Picture_x005f_x0020_3" src="cid:image002.jpg@01CADD59.3F08A740"
alt="cid:image003.jpg@01CAA0E0.B7CEC3E0"><o:p></o:p></p>
<p class=MsoNormal style='margin-left:35.4pt'>I have a number of questions
about the appropriateness of applying bootstrapping to our specific dataset:<o:p></o:p></p>
<p class=MsoListParagraph style='margin-left:71.4pt;text-indent:-.25in;
mso-list:l0 level1 lfo2'><![if !supportLists]><span style='mso-list:Ignore'>1)<span
style='font:7.0pt "Times New Roman"'> </span></span><![endif]>Because
we use wavelets for spectral decomposition (with frequency-dependent changes in
spectral and temporal resolution) is it valid to simply cluster across
different frequencies?<o:p></o:p></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'>Yes
it is. However, with your 20 sec. trials, I would not go for the high temporal
resolution that he wavelet transform gives you. I would do one Fourier-based
analyses for the first 2 seconds (encoding stage) and another one for the rest
of the trial (retention stage).<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoListParagraph style='margin-left:71.4pt;text-indent:-.25in;
mso-list:l0 level1 lfo2'><![if !supportLists]><span style='mso-list:Ignore'>2)<span
style='font:7.0pt "Times New Roman"'> </span></span><![endif]>We
are interested in comparing different conditions, where each is computed
relative to its own baseline. Is there anything wrong with using the
baselines of the same dataset for the null distribution as opposed to using a
different set of baseline data?<o:p></o:p></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'>Do
not baseline correct your data. Compare the raw power spectra for the correct
response trials with those of the incorrect response condition.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoListParagraph style='margin-left:71.4pt;text-indent:-.25in;
mso-list:l0 level1 lfo2'><![if !supportLists]><span style='mso-list:Ignore'>3)<span
style='font:7.0pt "Times New Roman"'> </span></span><![endif]>The
data have been recorded at 1KHz, and this oversampling results in high
spatial-frequency noise. Do I need to do any downsampling/smoothing
before applying the statistics?<o:p></o:p></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'>No.
However, with such long trials, I would definitely smooth in the frequency
domain using multitapers (also available in Fieldtrip).<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoListParagraph style='margin-left:71.4pt;text-indent:-.25in;
mso-list:l0 level1 lfo2'><![if !supportLists]><span style='mso-list:Ignore'>4)<span
style='font:7.0pt "Times New Roman"'> </span></span><![endif]>For
evaluating the relationship between channels, we compute the phase-locking value
(PLV), which has no meaningful single-trial measuremetnt. Is there any
way to apply statistical analyses directly to the average TF plots without
resorting back to the individual trials?<o:p></o:p></p>
<p class=MsoNormal><span style='font-size:10.5pt;font-family:Consolas;
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'>Have
look at the paper by Maris, Schoffelen, and Fries (2007, JNM) that describes
cluster-based permutation tests for coherence differences. This may be what you
need.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'>Best,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Verdana","sans-serif";color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.5pt;font-family:Consolas'>__________________________________________________________________________________</span><o:p></o:p></p>
<p class=MsoNormal>Allen Ardestani Email: <a
href="mailto:aardesta@ucla.edu">aardesta@ucla.edu</a><o:p></o:p></p>
<p class=MsoNormal>Phone: (310) 825-5528<o:p></o:p></p>
<p class=MsoNormal>Medical Scientist Training Program<o:p></o:p></p>
<p class=MsoNormal>David Geffen School of Medicine at UCLA<o:p></o:p></p>
<p class=MsoNormal>Semel Institute for Neuroscience and Human Behavior<o:p></o:p></p>
<p class=MsoNormal>760 Westwood Plaza<o:p></o:p></p>
<p class=MsoNormal>Los Angeles, CA 90095-1759<o:p></o:p></p>
<p class=MsoNormal>USA<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p><span lang=NL>----------------------------------<o:p></o:p></span></p>
<p><span lang=NL>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></p>
<p><span lang=NL>http://listserv.surfnet.nl/archives/fieldtrip.html<o:p></o:p></span></p>
<p><span lang=NL>http://www.ru.nl/fcdonders/fieldtrip/<o:p></o:p></span></p>
<p>----------------------------------<o:p></o: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.<o:p></o:p></p>
<p>http://listserv.surfnet.nl/archives/fieldtrip.html<o:p></o:p></p>
<p>http://www.ru.nl/fcdonders/fieldtrip/<o:p></o:p></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>