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Hi Jinhan,
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<div class="">I assume that you have first tried a 3D visualization (i.e. cfg.method = ‘ortho’ in ft_sourceplot) and ensured that everything looks OK with respect to coregistration with the anatomical image that you use for plotting, and also with respect to
the metric units? Note that everything needs to be consistent, for the source reconstruction, and the visualization, to make sense.</div>
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<div class="">Best wishes,</div>
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<div>Jan-Mathijs</div>
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<blockquote type="cite" class="">
<div class="">On 17 Jan 2024, at 16:15, Park, Jinhan via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
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<div class="elementToProof" 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;">
<span style="letter-spacing: normal; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; font-weight: 400;" class="">Hello, </span></div>
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<span style="letter-spacing: normal; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; font-weight: 400;" class=""><br class="">
</span></div>
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</div>
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<span style="letter-spacing: normal; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; font-weight: 400;" class="">I am Jinhan Park, a third-year Ph.D. Candidate at the University of Florida. I am
currently working on the analysis of resting-state EEG data with eyes closed in the source space. For the data analysis, I employed EEGLAB for preprocessing, ICA, and dipole fitting with independent components. The processed datasets were then transformed
into the FieldTrip format for source localization (eLORETA).</span></div>
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<span style="letter-spacing: normal; font-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; font-size: 15px; color: rgb(36, 36, 36); font-weight: 400;" class=""><br class="">
</span></div>
<div 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="letter-spacing: normal; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255); font-weight: 400;" class="">I created a source model using 'ft_prepare_leadfield'
and obtained distributed dipoles' power values using 'ft_sourceanalysis'. With this data, I attempted to visualize a 3D brain figure using 'ft_sourceplot' with the surface method. However, I noticed that certain areas of the brain appeared empty, and despite
their size being relatively small, it's causing some inconvenience. I've heard that this issue can potentially be addressed by interpolating the distributed values, but I'm uncertain about how to proceed.</span></div>
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</span></div>
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<div 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-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; text-align: left; background-color: rgb(255, 255, 255); margin: 0px;" class="">
<span style="letter-spacing: normal; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; font-weight: 400;" class="">Could you please let me know how to fix this problem? </span></div>
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</span></div>
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<span style="letter-spacing: normal; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; font-weight: 400;" class="">By the way, I wrote down some codes I did. </span></div>
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<span style="letter-spacing: normal; color: rgb(0, 128, 19);" class="">% Source model</span></div>
<div style="text-align: left; margin: 0px; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-size: 10pt;" class="">
<span style="letter-spacing: normal;" class="">vol = lo<i class="">ad(</i></span><span style="letter-spacing: normal; color: rgb(167, 9, 245);" class=""><i class="">'-mat'</i></span><span style="letter-spacing: normal;" class=""><i class="">, EEG.dipfit.hdmfile);</i></span><span style="letter-spacing: normal; color: rgb(0, 128, 19);" class=""><i class="">%
Load headfile from EEGLAB data processed by DIFIT</i></span></div>
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<span style="letter-spacing: normal;" class=""><i class="">cfg = [];</i></span></div>
<div style="text-align: left; margin: 0px; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-size: 10pt;" class="">
<span style="letter-spacing: normal;" class=""><i class="">cfg.elec = dataPre.elec;</i></span><span style="letter-spacing: normal; color: rgb(0, 128, 19);" class=""><i class="">% Channels' information</i></span></div>
<div style="text-align: left; margin: 0px; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-size: 10pt;" class="">
<span style="letter-spacing: normal;" class=""><i class="">cfg.headmodel = vol.vol;</i></span><span style="letter-spacing: normal; color: rgb(0, 128, 19);" class=""><i class="">% Headmodel</i></span></div>
<div style="text-align: left; margin: 0px; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-size: 10pt;" class="">
<span style="letter-spacing: normal;" class=""><i class="">cfg.resolution = 10; <span class="Apple-converted-space"> </span></i></span><span style="letter-spacing: normal; color: rgb(0, 128, 19);" class=""><i class="">% use a 3-D grid with a 1 cm resolution</i></span></div>
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<span style="letter-spacing: normal;" class=""><i class="">cfg.unit =<span class="Apple-converted-space"> </span></i></span><span style="letter-spacing: normal; color: rgb(167, 9, 245);" class=""><i class="">'mm'</i></span><span style="letter-spacing: normal;" class=""><i class="">;</i></span><span style="letter-spacing: normal; color: rgb(0, 128, 19);" class=""><i class="">%
Unit of voxels</i></span></div>
<div style="text-align: left; margin: 0px; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-size: 10pt;" class="">
<span style="letter-spacing: normal;" class=""><i class="">cfg.channel = {<span class="Apple-converted-space"> </span></i></span><span style="letter-spacing: normal; color: rgb(167, 9, 245);" class=""><i class="">'all'<span class="Apple-converted-space"> </span></i></span><span style="letter-spacing: normal;" class=""><i class="">};</i></span><span style="letter-spacing: normal; color: rgb(0, 128, 19);" class=""><i class="">%
Channels of interest</i></span></div>
<div style="text-align: left; margin: 0px; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-size: 10pt;" class="">
<span style="letter-spacing: normal;" class=""><i class="">cfg.normalize =</i></span><span style="letter-spacing: normal; color: rgb(167, 9, 245);" class=""><i class="">'yes'</i></span><span style="letter-spacing: normal;" class=""><i class="">;</i></span></div>
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<span style="letter-spacing: normal;" class=""><i class="">sourcemod</i>el = ft_prepare_leadfield(cfg);</span><span style="letter-spacing: normal; color: rgb(0, 128, 19);" class="">% Create a source model (leadfield)</span></div>
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<span style="letter-spacing: normal; color: rgb(0, 128, 19);" class="">%% Inverse solution</span></div>
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<span style="letter-spacing: normal; color: rgb(0, 128, 19);" class="">% eLORETA</span></div>
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<span style="letter-spacing: normal;" class="">cfg = [];</span></div>
<div style="text-align: left; margin: 0px; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-size: 10pt;" class="">
<span style="letter-spacing: normal;" class="">cfg.method =<span class="Apple-converted-space"> </span></span><span style="letter-spacing: normal; color: rgb(167, 9, 245);" class="">'eloreta'</span><span style="letter-spacing: normal;" class="">;</span><span style="letter-spacing: normal; color: rgb(0, 128, 19);" class="">%
Method for source localization</span></div>
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<span style="letter-spacing: normal;" class="">cfg.sourcemodel = sourcemodel;</span><span style="letter-spacing: normal; color: rgb(0, 128, 19);" class="">% Put the leadfield</span></div>
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<span style="letter-spacing: normal;" class="">cfg.headmodel = vol.vol;</span><span style="letter-spacing: normal; color: rgb(0, 128, 19);" class="">% Headmodel</span></div>
<div style="text-align: left; margin: 0px; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-size: 10pt;" class="">
<span style="letter-spacing: normal;" class="">source = ft_sourceanalysis(cfg, freq_pow);</span><span style="letter-spacing: normal; color: rgb(0, 128, 19);" class="">% Conduct the inverse solution. freq_pow is the power values in the frequency domain.</span></div>
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<span style="letter-spacing: normal;" class="">source_paf = source;</span></div>
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<span style="letter-spacing: normal;" class="">source_paf.avg.pow = dominant_f;</span><span style="letter-spacing: normal; color: rgb(0, 128, 19);" class="">% Change original PSD values (1 to 40 Hz) to peak frequencies</span></div>
<div style="text-align: left; margin: 0px; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-size: 10pt;" class="">
<span style="letter-spacing: normal;" class="">cfg = [];</span></div>
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<span style="letter-spacing: normal;" class="">cfg.method =<span class="Apple-converted-space"> </span></span><span style="letter-spacing: normal; color: rgb(167, 9, 245);" class="">'surface'</span><span style="letter-spacing: normal;" class="">;</span><span style="letter-spacing: normal; color: rgb(0, 128, 19);" class="">%
3D brain image</span></div>
<div style="text-align: left; margin: 0px; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-size: 10pt;" class="">
<span style="letter-spacing: normal;" class="">cfg.funparameter =<span class="Apple-converted-space"> </span></span><span style="letter-spacing: normal; color: rgb(167, 9, 245);" class="">'pow'</span><span style="letter-spacing: normal;" class="">;</span><span style="letter-spacing: normal; color: rgb(0, 128, 19);" class="">%
Represent "sourceoi.avg.pow"</span></div>
<div style="text-align: left; margin: 0px; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-size: 10pt;" class="">
<span style="letter-spacing: normal;" class="">cfg.maskparameter = cfg.funparameter;</span></div>
<div style="text-align: left; margin: 0px; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-size: 10pt;" class="">
<span style="letter-spacing: normal;" class="">cfg.funcolormap =<span class="Apple-converted-space"> </span></span><span style="letter-spacing: normal; color: rgb(167, 9, 245);" class="">'jet'</span><span style="letter-spacing: normal;" class="">;</span><span style="letter-spacing: normal; color: rgb(0, 128, 19);" class="">%
Types of the colorbar </span></div>
<div style="text-align: left; margin: 0px; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-size: 10pt;" class="">
<span style="letter-spacing: normal;" class="">cfg.projmethod =<span class="Apple-converted-space"> </span></span><span style="letter-spacing: normal; color: rgb(167, 9, 245);" class="">'nearest'</span><span style="letter-spacing: normal;" class="">;</span></div>
<div style="text-align: left; margin: 0px; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-size: 10pt;" class="">
<span style="letter-spacing: normal;" class="">cfg.surffile =<span class="Apple-converted-space"> </span></span><span style="letter-spacing: normal; color: rgb(167, 9, 245);" class="">'surface_white_both.mat'</span><span style="letter-spacing: normal;" class="">;</span><span style="letter-spacing: normal; color: rgb(0, 128, 19);" class="">%
Brain tamplate</span></div>
<div style="text-align: left; margin: 0px; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-size: 10pt;" class="">
<span style="letter-spacing: normal;" class="">cfg.surfdownsample = 10;</span><span style="letter-spacing: normal; color: rgb(0, 128, 19);" class="">% Downsample the voxels</span></div>
<div style="text-align: left; margin: 0px; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-size: 10pt;" class="">
<span style="letter-spacing: normal;" class="">ft_sourceplot(cfg, source_paf);</span><span style="letter-spacing: normal; color: rgb(0, 128, 19);" class="">% Plot the eLORETA figure</span></div>
</div>
<div style="text-align: left;" class=""><span style="letter-spacing: normal; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; font-weight: 400;" class="">I would sincerely appreciate it if you could
answer my question. </span></div>
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<span style="letter-spacing: normal; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; font-weight: 400;" class=""><br class="">
</span></div>
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<span style="letter-spacing: normal; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; font-weight: 400;" class="">Best regards, </span></div>
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<span style="letter-spacing: normal; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; font-weight: 400;" class="">Jinhan</span></div>
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<span style="font-size: 12pt;" class=""> </span></p>
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<span style="font-size: 12pt;" class=""><b class="">Jinhan Park (Hans) | Ph.D. candidate</b></span></div>
<div style="margin: 0in; font-family: Calibri, sans-serif; font-size: 11pt;" class="">
<span style="font-size: 12pt;" class="">Department of Applied Physiology and Kinesiology</span></div>
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<span style="font-size: 12pt;" class="">University of Florida</span></div>
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<span style="font-size: 12pt;" class="">Laboratory of Rehabilitation Neuroscience |<span class="Apple-converted-space"> </span><a href="https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flrnlab.org%2F&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C6db815f76c1444606bde08dc18446aad%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638411929313261006%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=EIDAhCVlnQK9OZ9DiyxKeT%2Fatu1eYlTbQ4XPCS49HvI%3D&reserved=0" originalsrc="http://lrnlab.org/" shash="F5JcS6XVjwkF1ErzH9eAJWJPbroSGI1grniyP7djPyJVLeWoN0sA36OcVwEdtBMqmg+aoi3o1Id8hujMtss+F5SnEu8op2U5W+UwvWJAmjWuUbqmlvga7IdkJgdHR+chcAUtDoMP5DIX1UOChdkimouS9uBZ2fm8sN7OjSUTIIs=" class="">lrnlab.org</a></span></div>
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<a href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C6db815f76c1444606bde08dc18446aad%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638411929313261006%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=AObD6Lc2MOMPBIENScnuoYLTAwxNpegPAl5GUgNfONU%3D&reserved=0" originalsrc="https://doi.org/10.1371/journal.pcbi.1002202" shash="sdvZHE88vuInfl+xe7c1gYe3A6OmeeKqs0UghbrApJYzOi6KmuHWktsFjTvt69uUJh2FNWkHendkVroDoo42nX4ZATgPh0lzDqrewV774vGdHHl4uGOxcByKBgxPJ5a9bYsmiDQHcG0RwRAWKRjSO73hvu0sS0ry1R3d/e9n24I=" 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>
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