<div dir="ltr"><div>Dear Jan,</div><div><br></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px">Your first trial only has a single sample. It is impossible to spectrally transform a single sample time course, this causes all kinds of low-level errors, the one you reported below.<br><br></blockquote>No, not quite. Let me explain myself again: ft_selectdata is outputting one sample and one value for the first trial alone when using the short latency. It is not the case that the first trial had only one sample in the input data to begin with. <div><br></div><div>Here's the input to ft_selectdata:<div><br></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div>data = </div></blockquote><div><br></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div> struct with fields:</div></blockquote></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><br></div></blockquote></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div> fsample: 1024</div></blockquote></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div> trial: {1×117 cell}</div></blockquote></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div> time: {1×117 cell}</div></blockquote></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div> label: {100×1 cell}</div></blockquote></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div> cfg: [1×1 struct]</div></blockquote></div></blockquote></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><br></div></blockquote><div><blockquote style="margin:0 0 0 40px;border:none;padding:0px">data.trial<br><br>ans =<br> 1×117 cell array<br> Columns 1 through 9<br><br> {100×1251 double} {100×1251 double} {100×1251 double} {100×1251 double} ......<br><br>data.time<br><br>ans =<br> 1×117 cell array<br> Columns 1 through 10<br><br> {1×1251 double} {1×1251 double} {1×1251 double} {1×1251 double} .......<br></blockquote><div><br></div>As you can see, the first trial is just fine and looks like any other trial. When I call ft_selectdata with cfg.latency = 0:1, this is the output data (below). Note that the function works as expected shortening the time vector to the desired length/latency for all trials. </div><div><br></div></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div>data.trial</div></div></blockquote><br><blockquote style="margin:0 0 0 40px;border:none;padding:0px">ans =</blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"> 1×117 cell array</blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"> Columns 1 through 9</blockquote><br><blockquote style="margin:0 0 0 40px;border:none;padding:0px"> {100×251 double} {100×251 double} {100×251 double} {100×251 double}</blockquote><div><div><br></div></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div>data.time</div></div></blockquote><div><div><br></div></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div>ans =</div></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div> 1×117 cell array</div></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div> Columns 1 through 11</div></div></blockquote><div><div><br></div></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div> {1×251 double} {1×251 double} {1×251 double} {1×251 double} </div></div></blockquote><div><div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><br></blockquote>However, this is the output if I use any cfg.latency parameter shorter than one second (e.g. .15-.25, 0-.5, .5-1, etc). As you can see in that case, ft_selectdata operates in the first trial alone in an unexpected manner.</div><div><br></div></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div>data.trial</div></div></blockquote><div><div><br></div></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div>ans =</div></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div> 1×117 cell array</div></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div> Columns 1 through 9</div></div></blockquote><div><div><br></div></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div> {100×1 double} {100×1251 double} {100×1251 double} {100×1251 double}</div></div></blockquote><div><div><br></div></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div>data.time</div></div></blockquote><div><div><br></div></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div>ans =</div></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div> 1×117 cell array</div></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div> Columns 1 through 10</div></div></blockquote><div><div><br></div></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div> {[0.1480]} {1×1251 double} {1×1251 double} {1×1251 double}</div></div></blockquote><div><div><br></div><div><br></div><div>So my question is whether there is any reason why ft_selectdata behaves like this when using cfg.latency parameters shorter than one second. Sorry if I wasn't clear enough.</div><div><br></div><div>Best,</div><div><br><div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><b><font size="4">Sergio A. Osorio</font></b><div><div>Laboratory for Cognitive and Evolutionary Neuroscience<br></div><div>Center for Medical Research - Faculty of Medicine</div></div>Pontificia Universidad Católica de Chile<div><b><font size="4"><img src="https://docs.google.com/uc?export=download&id=1OQHsbxZhdStfXHspAWfa0MDdBX9f6jXb&revid=0BzBWIjzXUIlcamV1a20wbWc0T3ZtM1JqdjRuUzNqV1psV3FzPQ" width="200" height="87"></font></b><div><br><div></div><div></div></div></div></div></div></div><br></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El jue, 23 sept 2021 a las 4:07, Schoffelen, J.M. (Jan Mathijs) via fieldtrip (<<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>>) escribió:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="overflow-wrap: break-word;">
Hi Sergio,
<div><br>
</div>
<div>Yes, you are doing something wrong:</div>
<div><br>
<div>
<blockquote type="cite">
<div>
<div dir="ltr" style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<div><font> % select the portion of the data I want to compute the wPLI for </font></div>
<div><font> cfg = [ ];<br>
cfg.latency = .15:.25; <<<<<<<<<<<<<< if I use 0:1 or 1:1.5,<span> </span><i>ft_freqanaylisis</i><span> </span>runs without any problem, but if I use any
other latency within 1 second it doesn't work.<br>
data = ft_selectdata(cfg,data);</font></div>
<div><font> </font></div>
<div><font> % here's the output structure</font></div>
<div>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font>data =</font></div>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font><br>
</font></div>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<font>struct with fields:<br>
</font></blockquote>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font><br>
</font></div>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font> fsample: 250</font></div>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font> trial: {1×117 cell}</font></div>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font> time: {1×117 cell}</font></div>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font> label: {100×1 cell}</font></div>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font> cfg: [1×1 struct]</font></div>
<div><font><br>
</font></div>
<div>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<font>data.trial<br>
</font></blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font><br>
ans =<br>
1×117 cell array<br>
Columns 1 through 9<br>
<br>
</font></div>
</blockquote>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font> {100×1 double} {100×1251 double} {100×1251 double} % averaged first trial in the 2nd dimension instead of selecting the time interval of interest</font></div>
</blockquote>
</blockquote>
</blockquote>
</div>
</blockquote>
</blockquote>
</div>
</div>
</div>
</blockquote>
<div><br>
</div>
<div><br>
</div>
<div>Your first trial only has a single sample. It is impossible to spectrally transform a single sample time course, this causes all kinds of low-level errors, the one you reported below.</div>
<div><br>
</div>
<div>I don’t know what you mean with the statement that ft_selectdata does not work with ‘any other latency within 1 second’, but I suggest you first inspect your data, and specifically the time axes of the individual trials. </div>
<div><br>
</div>
<div>Best wishes,</div>
<div>Jan-Mathijs</div>
<div><br>
</div>
<div><br>
</div>
<br>
<blockquote type="cite">
<div>
<div dir="ltr" style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<div>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font><br>
</font></div>
</blockquote>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<font>data.time<br>
</font></blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font>ans =<br>
1×117 cell array<br>
Columns 1 through 10<br>
<br>
</font></div>
</blockquote>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font> {[0.1480]} {1×1251 double} {1×1251 double}</font></div>
</blockquote>
</blockquote>
</blockquote>
</div>
</blockquote>
</blockquote>
<font> <span> </span><br>
% Now call the ft_freqanalysis function<span> </span><br>
cfg = [ ];<br>
cfg.output = 'fourier';<br>
cfg.method = 'mtmfft';<br>
cfg.taper = 'dpss';<br>
cfg.foi = linspace(1,31,60);<br>
cfg.tapsmofrq = 4;<br>
tf_data = ft_freqanalysis(cfg,data);</font></div>
<div><font><br>
</font></div>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font>Error using dpss>parseinputs (line 308)</font></div>
<div><font>Time-bandwidth product NW must be a positive number.</font></div>
</blockquote>
<div><font><br>
</font></div>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font>Error in dpss (line 62)</font></div>
<div><font>[method,k,Ni,traceFlag,N,NW] = parseinputs(N,NW,varargin{:});</font></div>
</blockquote>
<div><font><br>
</font></div>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font>Error in ft_specest_mtmfft>double_dpss (line 362)</font></div>
<div><font>tap = dpss(double(a), double(b), varargin{:});</font></div>
</blockquote>
<div><font><br>
</font></div>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font>Error in ft_specest_mtmfft (line 151)</font></div>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font> tap = double_dpss(ndatsample,ndatsample*(tapsmofrq./fsample))';</font></div>
</blockquote>
<div><font><br>
</font></div>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font>Error in ft_freqanalysis (line 563)</font></div>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font> [spectrum,ntaper,foi] = ft_specest_mtmfft(dat, time, 'taper', cfg.taper, options{:}, 'feedback', fbopt);</font></div>
</blockquote>
<div><font><br>
</font></div>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font>Error in Connectivity_wPLI (line 68)</font></div>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><font> tf_data = ft_freqanalysis(cfg,data);</font></div>
</blockquote>
<div><br>
</div>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<br>
</blockquote>
<div>All best,</div>
<div><br>
</div>
<div>
<div>
<div dir="ltr">
<div dir="ltr"><font size="4"><b>Sergio. </b></font><br>
<div>
<div><br>
<div></div>
<div></div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
</div>
<br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<div class="gmail_quote" style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<div dir="ltr" class="gmail_attr">El mié, 15 sept 2021 a las 15:09, SERGIO OSORIO GALEANO (<<a href="mailto:srosorio@uc.cl" target="_blank">srosorio@uc.cl</a>>) escribió:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div>Yes, you made a mistake in the (assumptions underlying) the implementation: the cfg.toi that you supply before ft_freqanalysis is not going to have any effect if you use ‘mtmfft’ as a method, since this method just provides a single estimate of
the spectrum using the whole ’trial’ for the estimation.</div>
</blockquote>
<div><br>
</div>
Oh, that makes perfect sense. Cheers Jan! Really appreciate it.
<div><b><br clear="all">
</b>
<div>
<div dir="ltr">
<div dir="ltr"><b>Sergio.</b>
<div>
<div><br>
<div></div>
<div></div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">El mié, 15 sept 2021 a las 14:29, Schoffelen, J.M. (Jan Mathijs) via fieldtrip (<<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>>) escribió:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Hi Sergio,<br>
><span> </span><br>
> 1) Regardless of whether I use my full time window of interest (0-1.5 s) or whether I estimate wPLI for two separate shorter time windows (0-.7 s and .7-1.5 s), the results are always identical to one another. Is this normal behaviour in wPLI analyses or
is there something potentially wrong with how I've implemented it?<span> </span><br>
<br>
Yes, you made a mistake in the (assumptions underlying) the implementation: the cfg.toi that you supply before ft_freqanalysis is not going to have any effect if you use ‘mtmfft’ as a method, since this method just provides a single estimate of the spectrum
using the whole ’trial’ for the estimation.<br>
<br>
> 2) I notice that wPLI values are way lower for low-frequencies (4-7hz) than for higher-frequencies (8-12hz and 15-30hz). While this could be a real effect associated with my task, the fact that this result is consistent across different conditions makes me
wonder whether I've done something wrong in the ft_freqanalysis configuration.<span> </span><br>
<br>
I think that this is just a property of the data.<br>
<br>
Best wishes,<br>
Jan-Mathijs<br>
<br>
<br>
><span> </span><br>
> Thanks a lot in advance for any help anyone can provide!<span> </span><br>
><span> </span><br>
> -----------<br>
><span> </span><br>
> cfg = [ ];<br>
> data = ft_preprocessing(cfg,rwdata);<br>
> <br>
> %resample data<br>
> cfg = [ ];<br>
> cfg.resamplefs = 250;<br>
> data = ft_resampledata(cfg, data);<br>
><span> </span><br>
> data =<br>
> struct with fields:<br>
><span> </span><br>
> fsample: 250<br>
> trial: {1×117 cell}<br>
> time: {1×117 cell}<br>
> label: {100×1 cell}<br>
> cfg: [1×1 struct]<br>
> <br>
> % next, call the ft_freqanalysis function in our source data<br>
> cfg = [ ];<br>
> cfg.output = 'fourier';<br>
> cfg.method = 'mtmfft';<br>
> cfg.taper = 'dpss';<br>
> cfg.foi = linspace(4,30,30);<br>
> cfg.tapsmofrq = 4;<br>
> cfg.toi = 0:.02:1.5; % try 0:.02:.7 and .7:.02:1.5<br>
> tf_data = ft_freqanalysis(cfg,data);<br>
><span> </span><br>
> tf_data =<span> </span><br>
> struct with fields:<br>
><span> </span><br>
> label: {100×1 cell}<br>
> dimord: 'rpttap_chan_freq'<br>
> freq: [1×30 double]<br>
> fourierspctrm: [4563×100×30 double]<br>
> cumsumcnt: [117×1 double]<br>
> cumtapcnt: [117×1 double]<br>
> cfg: [1×1 struct]<br>
> <br>
> % estimate wPLI values<br>
> cfg = [ ];<br>
> cfg.method = 'wpli_debiased';<span> </span><br>
> connect_data = ft_connectivityanalysis(cfg,tf_data);<br>
><span> </span><br>
> connect_data =<span> </span><br>
> struct with fields:<br>
><span> </span><br>
> label: {100×1 cell}<br>
> dimord: 'chan_chan_freq'<br>
> wpli_debiasedspctrm: [100×100×30 double]<br>
> freq: [1×30 double]<br>
> cfg: [1×1 struct]<br>
><span> </span><br>
> Best,<br>
><span> </span><br>
> Sergio.<br>
><span> </span><br>
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<span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">fieldtrip
mailing list</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline"><a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<a href="https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!usewI1PbndK5LPja3Ngfqvfn3tRpdRV73OimKW6NrcohdNrX6G3vkgQuzYR9QRioc7pHSLvRNfscdfs$" style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!usewI1PbndK5LPja3Ngfqvfn3tRpdRV73OimKW6NrcohdNrX6G3vkgQuzYR9QRioc7pHSLvRNfscdfs$</a><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline"></span></div>
</blockquote>
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</div>
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_______________________________________________<br>
fieldtrip mailing list<br>
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" rel="noreferrer" target="_blank">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
<a href="https://doi.org/10.1371/journal.pcbi.1002202" rel="noreferrer" target="_blank">https://doi.org/10.1371/journal.pcbi.1002202</a><br>
</blockquote></div>