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Hi Marta,
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<div class="">I must say that I don’t understand the question behind your question. What is it you want to achieve? You mention that you wish to know about (QUOTE) "<span style="background-color: white;" class=""><font face="Calibri, sans-serif" class=""><span style="font-size: 11pt;" class="">the
most effective way to replicate this output/reshape the output of ft_virtualchannel or somehow with ft_virtualchannel in the easiest possible way obtain one value per parcel</span><span style="font-size: 14.666666984558105px;" class="">”</span><span style="font-size: 11pt;" class="">.
And then you mention a few data structures that in part seem to have been handcrafted. What is it what you want to achieve? Are you sure that ft_virtualchannel is the function you want to use? Is the question underlying your question related to visualization,
statistics, something else?</span></font></span></div>
<div class=""><span style="background-color: white;" class=""><font face="Calibri, sans-serif" class=""><span style="font-size: 11pt;" class=""><br class="">
</span></font></span></div>
<div class=""><span style="background-color: white;" class=""><font face="Calibri, sans-serif" class=""><span style="font-size: 11pt;" class="">The purpose of ft_virtualchannel - as it</span><span style="font-size: 14.666666984558105px;" class="">’</span><span style="font-size: 11pt;" class="">s
name suggests - is to create a data structure that contains virtual channels, i.e. a representation of data that behaves as if it</span><span style="font-size: 14.666666984558105px;" class="">’</span><span style="font-size: 11pt;" class="">s channel level
data, but now with each of the channels representing time series (or frequency domain fourier spectra) mapped onto a location/parcel in source space. The output of ft_virtualchannel can be further processed to obtain derived quantities from the time series,
e.g. a value that represent the power in a particular frequency band, for instance the alpha band. In order to obtain that, one would run ft_freqanalysis on the output of ft_virtualchannel, and e.g. followed by ft_selectdata with a specified frequency range,
and avgoverfreq = </span><span style="font-size: 14.666666984558105px;" class="">‘</span><span style="font-size: 11pt;" class="">yes</span><span style="font-size: 14.666666984558105px;" class="">’. Then, in order to visualize the result, one would require
the mapping from the individual virtual channels to the original source space, which is represented in the brainordinate field, which in your case seems to be a low resolution 3D-grid based representation of an anatomical atlas that is defined on a volume.</span></font></span></div>
<div class=""><span style="background-color: white;" class=""><font face="Calibri, sans-serif" class=""><span style="font-size: 14.666666984558105px;" class=""><br class="">
</span></font></span></div>
<div class=""><span style="background-color: white;" class=""><font face="Calibri, sans-serif" class=""><span style="font-size: 14.666666984558105px;" class="">I don’t know by heart what (and whether there exists any) the smoothest procedure will be for visualization
in FT. If there is no mention anywhere in the documentation to visualize this easily, I suspect that you need to map the scalars back onto the original volume, and then you could use ft_sourceinterpolate to obtain a data structure that maps the low resolution
volume back onto a high resolution volume (containing a template anatomical image), so that you can visualize it in ft_sourceplot.</span></font></span></div>
<div class=""><span style="background-color: white;" class=""><font face="Calibri, sans-serif" class=""><span style="font-size: 14.666666984558105px;" class=""><br class="">
</span></font></span></div>
<div class=""><span style="background-color: white;" class=""><font face="Calibri, sans-serif" class=""><span style="font-size: 14.666666984558105px;" class="">Good luck, and happy computing,</span></font></span></div>
<div class=""><span style="background-color: white;" class=""><font face="Calibri, sans-serif" class=""><span style="font-size: 14.666666984558105px;" class="">Jan-Mathijs</span></font></span></div>
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</span></font></span></div>
<div class=""><span style="background-color: white;" class=""><font face="Calibri, sans-serif" class=""><span style="font-size: 11pt;" class=""><br class="">
</span></font></span></div>
<div class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 26 Jan 2023, at 17:53, Marta Stojanović via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
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<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class="">Hi, </span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class="">I hope this email finds you well. I have a question about obtaining one power value per parcel after using ft_virtualchannel. I guess there must be a way to create a dummy struct that could solve
this problem, so apologies if there is a straightforward answer, but I am finding it hard to obtain one value per parcel after interpolating source data onto an atlas and running ft_virtualchannel.</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class="">I run ft_virtualchannel instead of ft_sourceparcellate because I want to keep trial information which I couldn’t keep with the output of ft_sourceparcellate. The output of ft_virtualchannel that I
obtain through this looks like: </span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> struct with fields:</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> trial: [142×246×1018 double]</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> time: [1×1018 double]</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> dimord: 'rpt_chan_time'</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> label: {246×1 cell}</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> cfg: [1×1 struct]</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> grad: [1×1 struct]</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> sampleinfo: [142×2 double]</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> trialinfo: [142×2 double]</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> brainordinate: [1×1 struct]</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="EN-US" style="background-color: white;" class=""> </span><o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span style="" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class="">After I use some fields from a previously generated average of alpha power along with fields from the ft_virtualchannel output to create the following dummy source struct:</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> trial: [142×246 double]</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> time: 0</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> cfg: [1×1 struct]</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> dim: [26 33 28]</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> pos: [24024×3 double]</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> pow: [24024×1 double]</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class="">The data is collapsed across time, but the pow field is the multiplication of the dimensions of the tissue (26 * 33 * 28), rather than a value per parcel.</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class="">I know from the Fieldtrip tutorials online that the output of ft_sourceparcellate can look like this:</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span style="background-color: white;" class="">parcel =</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span style="background-color: white;" class=""> label: {1x116 cell} % brain parcels labels</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> </span><span style="background-color: white;" class=""> anatomy: [116x1 double]</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> </span><span style="background-color: white;" class="">anatomydimord: 'chan_unknown'</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span style="background-color: white;" class=""> pow: [116x1 double] % one value of brain activity per parcel</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> </span><span style="background-color: white;" class=""> powdimord: 'chan'</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> </span><span style="background-color: white;" class="">brainordinate: [1x1 struct]</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span style="background-color: white;" class=""> cfg: [1x1 struct]</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span style="background-color: white;" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span style="background-color: white;" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class="">I’m wondering if you could perhaps point me to the most effective way to replicate this output/reshape the output of ft_virtualchannel or somehow with ft_virtualchannel in the easiest possible way
obtain one value per parcel. Essentially, I’m most interested in replicating or obtaining the ‘pow’ field from the ft_sourceparcellate output where I would have one power or activity estimate per parcel.</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class="">I hope the question makes sense, and I can of course elaborate or explain further if not. Either way, thanks a lot in advance!</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class=""> </span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class="">All the best, </span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; background-color: white;" class="">
<span lang="EN-US" style="background-color: white;" class="">Marta</span><span style="" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
</div>
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<a href="https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!8FT62BXQNEdwl2ym7MPEQPvYBcvuo-W43pLyc6ErhtPG0h_Hp9l1IoqOijJMJZURZi3EiUNhvyTmqzhBhs0cuQQkEAHPRgVe3c7Egw$" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!8FT62BXQNEdwl2ym7MPEQPvYBcvuo-W43pLyc6ErhtPG0h_Hp9l1IoqOijJMJZURZi3EiUNhvyTmqzhBhs0cuQQkEAHPRgVe3c7Egw$</a><span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class=""></span></div>
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