<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
Hi Laura,
<div class=""><br class="">
</div>
<div class="">
<div>
<blockquote type="cite" class="">
<div class="">
<div id="divtagdefaultwrapper" dir="ltr" style="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; font-size: 12pt; font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class="">
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">I am currently doing artefact rejection on a dataset of children's EEG using ICA. I am able to plot the topography and timecourse of my ICA components, but fail in plotting their frequency-power spectrum
(lot's of alpha activity in my dataset. Hopefully loads into a single component).</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">I found some code snippets in old messages on the mailing list but have not been able to apply them on my dataset. Is there maybe a tutorial I missed, some code that shows how to plot the freq-pwer
spectrum like in eeglab?<span class="Apple-converted-space"> </span></div>
</div>
</div>
</blockquote>
<div><br class="">
</div>
<div>If you want to compute a powerspectrum for component time-series data, you’d want to call ft_freqanalysis on the output structure that you get after ft_componentanalysis, and then make a figure, using old-fashioned matlab, plot, or perhaps ft_singleplotER
(use cfg.method = ‘mtmfft’ for ft_freqanalysis)</div>
<div><br class="">
</div>
<blockquote type="cite" class="">
<div class="">
<div id="divtagdefaultwrapper" dir="ltr" style="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; font-size: 12pt; font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class="">
<div style="margin-top: 0px; margin-bottom: 0px;" class="">I also found ft_icabrowser(cfg, comp), which should plot the freq-power spectrum of my components alongside other measures. I tried using it like this, with a custom layout<br class="">
</div>
<p style="margin-top: 0px; margin-bottom: 0px;" class=""></p>
<div style="padding: 30px;" class="">
<div style="font-size: 10pt; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-style: normal; font-weight: normal;" class="">
<span style="white-space: pre;" class=""><span class="">cfg = [];</span></span></div>
<div style="font-size: 10pt; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-style: normal; font-weight: normal;" class="">
<span style="white-space: pre;" class=""><span class="">cfg.layout = <span class="">
'C:\EEG_Data\layout_EEG.mat'</span></span></span></div>
<div style="font-size: 10pt; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-style: normal; font-weight: normal;" class="">
<span style="white-space: pre;" class=""><span class="">[dummy] = ft_icabrowser(cfg, comp);</span></span></div>
</div>
however, instead of one figure window with several subplots per component, several windows are opened, each containing subplots, some of them empty. The topoplots also open in seperate windows and only the first 4 of my 25 components are plotted. For each component
I get this error message:
<p style="margin-top: 0px; margin-bottom: 0px;" class=""></p>
<p style="margin-top: 0px; margin-bottom: 0px;" class=""></p>
<div class="">Warning: could not determine dimord of "comp" in:<br class="">
<br class="">
label: {28×1 cell}<br class="">
cfg: [1×1 struct]<br class="">
topo: [28×1 double]<br class="">
topodimord: 'chan_comp'<br class="">
comp: 4<br class="">
unmixing: [-1.2657 -1.5088 -1.6876 -1.1454 -1.3345 0.0388 -0.3569 1.2782 0.3718 -1.7437 -1.7553 -1.5412 -0.1625 0.6848 -0.4991 -1.8822 -0.2463 -1.5501 -2.0003 … ]<br class="">
unmixingdimord: 'chan_topochan'</div>
<p style="margin-top: 0px; margin-bottom: 0px;" class=""></p>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Any thoughts on this?</div>
</div>
</div>
</blockquote>
<div><br class="">
</div>
<div>Not really, ft_icabrowser is a function which is based on an external contribution to fieldtrip, which has never made it into the core release part of the code base. The core release part is kept up to date by the developer’s team, but the more peripheral
functions are not. It could be that the advancing quality of the core FT-code has caused a backward compatibility break w.r.t. ft_icabrowser.</div>
<div><br class="">
</div>
<div>We can look into this (with not too high priority, because busy -> nudge to the stakeholders of the ft_icabrowser code to step in). For this we would appreciate you to file this as an issue on github:</div>
<div><a href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ffieldtrip%2Ffieldtrip&data=05%7C01%7Cfieldtrip%40science.ru.nl%7Cd344a60d6e3644c14e5908dbf6345e3c%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638374476996945168%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=7Gb2HYJ2d6UkDwdgId4edMqn%2B9qZVBmBHS%2F2zoCKtNM%3D&reserved=0" originalsrc="https://github.com/fieldtrip/fieldtrip" shash="los96WRfFgyQ0C0a6ASRH4z9aSlhiNL7O0B17WpNHaDl9oXAOnh20eE3NkUgAqeYjVgkKBDL+uUu7/Eeb/+2tt4RCxUrK8GlP1FcoZMuYAg3sKL11gfspjkA8thlPH/xbfVyA2TkcpGiQ1a5XCDDE8HPxFvaWWawBvVTsQ7ZPkM=" class="">https://github.com/fieldtrip/fieldtrip</a>,
describing the issue, provide some code and minimal data snippet for replication, and we can see how to take it from there.</div>
<div><br class="">
</div>
<div>Best wishes,</div>
<div>Jan-Mathijs</div>
<div><br class="">
</div>
<div><br class="">
</div>
<br class="">
<blockquote type="cite" class="">
<div class="">
<div id="divtagdefaultwrapper" dir="ltr" style="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; font-size: 12pt; font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class="">
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Thanks in advance and best wishes,</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Laura<br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div id="Signature" class="">
<div id="divtagdefaultwrapper" dir="ltr" style="font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 12pt;" class="">
<span style="font-family: Calibri, Helvetica, sans-serif;" class=""></span>
<div id="divtagdefaultwrapper" dir="ltr" style="font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 12pt;" class="">
<span style="font-family: Calibri, Helvetica, sans-serif;" class=""></span>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt; white-space: pre;" class="">__________</span></div>
<span style="font-family: Calibri, Helvetica, sans-serif;" class=""></span>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt; white-space: pre;" class="">Dr. Laura Hahn</span></div>
<span style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;" class=""></span>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt; white-space: pre;" class="">Forschungsgruppe Frühkindliche Sprachentwicklung</span></div>
<span style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;" class=""></span>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt; white-space: pre;" class="">Klinik für Audiologie und Phoniatrie</span></div>
<span style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;" class=""></span>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt; white-space: pre;" class=""><span style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;" class="">Charité -
Universitätsmedizin Berlin</span><span style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt; white-space: pre;" class="">
</span></span></div>
<span style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;" class=""></span>
<p style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt; white-space: pre;" class=""></span></p>
<span style="font-family: Calibri, Helvetica, sans-serif; font-size: 10pt;" class=""></span><br class="">
<p style="margin-top: 0px; margin-bottom: 0px;" class=""></p>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
</div>
</div>
</div>
</div>
<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><br 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;" class="">
<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="">fieldtrip
mailing list</span><br 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;" class="">
<a href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=05%7C01%7Cfieldtrip%40science.ru.nl%7Cd344a60d6e3644c14e5908dbf6345e3c%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638374476996945168%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=nKHia1nqL6c9iKxkk6DxU8hEUZ6%2BYmgVMObuoNLAEd0%3D&reserved=0" originalsrc="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" shash="jxu6/i516hU446S7jdYuC+7D64a7lhrrE2NMWNnYrJkAWorrmuJOTuM5oCU1TLUidtsXsqZmgxURRkIFxSPdnATscOKbqhWtUV89dKcII9Nj7lbhAqgKn+GmEkDzvulxHTKmw1MIWg3s7QmIXWaESAUbXZN0m0G5+bTN1+GKAg8=" 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://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br 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;" class="">
<a href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&data=05%7C01%7Cfieldtrip%40science.ru.nl%7Cd344a60d6e3644c14e5908dbf6345e3c%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638374476996945168%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=116JjGvkdMM%2BTQLMRgv8F7oqKGDJduQVkT4jCr6VMtU%3D&reserved=0" originalsrc="https://doi.org/10.1371/journal.pcbi.1002202" shash="XvKldEzN4sVUl3/0MP39OAsXEaXadn6rDzcD5/Ov8SOdJn959o/YcNuyNoTanrO4EBarvFXflhc1NuX/CoeOyVwgYuwrfhEExErIir8rCOKwRhJiZ+s41/0tGt83nu5sfA0SyV91xNbnEiIW1B6et8VZ0j7brn4FMUvd3RNRSJ4=" 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://doi.org/10.1371/journal.pcbi.1002202</a></div>
</blockquote>
</div>
<br class="">
</div>
</body>
</html>