<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style><![endif]--><style><!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:0 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:Courier;
panose-1:0 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:"MS Mincho";
panose-1:2 2 6 9 4 2 5 8 3 4;}
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:"Calibri Light";
panose-1:2 15 3 2 2 2 4 3 2 4;}
@font-face
{font-family:"\@MS Mincho";
panose-1:2 2 6 9 4 2 5 8 3 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p.msonormal0, li.msonormal0, div.msonormal0
{mso-style-name:msonormal;
margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
span.apple-converted-space
{mso-style-name:apple-converted-space;}
span.EmailStyle20
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:windowtext;}
p.p1, li.p1, div.p1
{mso-style-name:p1;
margin:0cm;
margin-bottom:.0001pt;
font-size:7.5pt;
font-family:Courier;}
p.p2, li.p2, div.p2
{mso-style-name:p2;
margin:0cm;
margin-bottom:.0001pt;
font-size:7.5pt;
font-family:Courier;
color:forestgreen;}
span.s1
{mso-style-name:s1;
color:black;}
span.s2
{mso-style-name:s2;
color:#A020F0;}
p.p3, li.p3, div.p3
{mso-style-name:p3;
margin:0cm;
margin-bottom:.0001pt;
font-size:7.5pt;
font-family:Courier;}
p.p4, li.p4, div.p4
{mso-style-name:p4;
margin:0cm;
margin-bottom:.0001pt;
font-size:9.0pt;
font-family:Courier;}
span.s3
{mso-style-name:s3;
color:forestgreen;}
span.s4
{mso-style-name:s4;
color:blue;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-NZ" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Hello Michael,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">I currently following a very similar path for analysing my EEG data with the following steps:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">%Load the template brain, MRI and EEG electrodes<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black">load (</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'biosemi32elec_aligned.mat'</span><span style="font-size:7.5pt;font-family:Courier;color:black">)
</span><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% electrodes have been manually aligned using the interface<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black">load (</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'leadfield6mm.mat'</span><span style="font-size:7.5pt;font-family:Courier;color:black">)</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black">load([FIELDTRIPDIR
</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'/template/headmodel/standard_bem.mat'</span><span style="font-size:7.5pt;font-family:Courier;color:black">]);
</span><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">%template boundary element model</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black">load([FIELDTRIPDIR
</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'/template/headmodel/standard_mri.mat'</span><span style="font-size:7.5pt;font-family:Courier;color:black">]);
</span><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">%template mri</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">atlas = ft_read_atlas([FIELDTRIPDIR
<span style="color:#A020F0">'/template/atlas/aal/ROI_MNI_V4.nii'</span>]);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">%Generate sourcemodel and leadfields (common for all data)<o:p></o:p></span></p>
<p class="p1"><span class="apple-converted-space"> </span>cfg = [];<o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span>cfg.headmodel = vol;<o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span>cfg.elec = elec_aligned;<o:p></o:p></p>
<p class="p2"><span class="apple-converted-space"><span style="color:black"> </span>
</span><span class="s1">cfg.grid.resolution = 6; </span><span class="apple-converted-space"><span style="color:black">
</span></span>% use a 3-D grid with a 6mm resolution<o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span>cfg.grid.unit <span class="apple-converted-space">
</span>= <span class="s2">'mm'</span>;<o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span>cfg.channel = 1:32;<o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span>grid = ft_prepare_leadfield(cfg);<o:p></o:p></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Load the data<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">%Calculate the channel covariance matrix for all exposures<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.covariance =
<span style="color:#A020F0">'yes'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.covariancewindow =
<span style="color:#A020F0">'all'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.keeptrials =
<span style="color:#A020F0">'yes'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> timelock_allexp = ft_timelockanalysis(cfg, data_filt);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">%Calculate the channel covariance matric for each exposure separate<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> timelock=cell(length(exposures));<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> <span style="color:blue">
for</span> j=1:length(exposures)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.covariance =
<span style="color:#A020F0">'yes'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.covariancewindow =
<span style="color:#A020F0">'all'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.trials = find(ismember(trialinfo, exposures{j}));<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.keeptrials =
<span style="color:#A020F0">'yes'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> timelock{j} = ft_timelockanalysis(cfg, data_filt);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> <span style="color:blue">
end</span><o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">%General source localisation<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.headmodel = vol;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.elec = elec_aligned;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.grid = grid;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.method =
<span style="color:#A020F0">'lcmv'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black"> cfg.lcmv.fixedori =
</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'yes'</span><span style="font-size:7.5pt;font-family:Courier;color:black">;
</span><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">%Project onto largest variance orientation<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.lcmv.keepfilter =
<span style="color:#A020F0">'yes'</span>; <span style="color:forestgreen">%Keep the beamformer weights</span><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.lcmv.lambda =
<span style="color:#A020F0">'5%'</span>; <span style="color:forestgreen">%Regularise a little</span><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> source_allexp = ft_sourceanalysis(cfg, timelock_allexp);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% source localisation for each exposure separate using combined filter<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.headmodel = vol;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.elec = elec_aligned;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.grid = grid;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black"> cfg.grid.filter = source_allexp.avg.filter;
</span><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% use the common filter computed in the previous step!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.method =
<span style="color:#A020F0">'lcmv'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black"> cfg.lcmv.fixedori =
</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'yes'</span><span style="font-size:7.5pt;font-family:Courier;color:black">;
</span><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">%Project onto largest variance orientation<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.lcmv.lambda =
<span style="color:#A020F0">'5%'</span>; <span style="color:forestgreen">%Regularise a little</span><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black"> cfg.rawtrial =
</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'yes'</span><span style="font-size:7.5pt;font-family:Courier;color:black">;
</span><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% project each single trial through the filter.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.keeptrials =
<span style="color:#A020F0">'yes'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> parc_sources=cell(length(exposures),1);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> <span style="color:blue">
for</span> j=1:length(exposures)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> source = ft_sourceanalysis(cfg, timelock{j});<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> source = ft_datatype_source(source);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.parameter =
<span style="color:#A020F0">'all'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> source_int = ft_sourceinterpolate(cfg, source, atlas);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.method =
<span style="color:#A020F0">'max'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> parc_sources{j}=ft_sourceparcellate(cfg, source_int, atlas);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> <span style="color:blue">
end</span><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> </span><span style="mso-fareast-language:EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">I hope my code for source parcellation helps to solve your problem.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Xavier<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">fieldtrip <fieldtrip-bounces@science.ru.nl> on behalf of Michael Glassen - Biomedical Engineer <MGlassen@kesslerfoundation.org><br>
<b>Reply to: </b>FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Date: </b>Saturday, 16 May 2020 at 8:42 AM<br>
<b>To: </b>FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Subject: </b>[FORGED] Re: [FieldTrip] Computing source-level ROI EEG connectivity<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div id="divtagdefaultwrapper">
<div id="divtagdefaultwrapper">
<p><span style="font-size:12.0pt;color:black">Dear Fieldtrip Community,<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black">I implemented most of the changes you all suggested and some that you didn't, and I am still getting some odd results, but in a different way. At the end of my pipeline I am computing bivariate granger causality
over all ROIs in the volumetric AAL atlas provided with fieldtrip. ft_sourceparcellate gives me errors when trying to use, so to project sources onto ROIs I interpolate the AAL atlas onto my sourcemodel using ft_sourceinterpolate. I then go through each ROI
and create a binary mask of voxels, which I then use to average the moms together to get ROI source activity. Before this step I use the svd method to pick a principal component of each voxel. When I plot a heatmap of these results averaged over the beta band(12-30
Hz), most roi pairs have a granger value between 0.1-0.3, but there are certain rois that have a very high granger across a ton of regions(>1). This happened with multiple datasets from different studies. I suspect that the issue(if these is one) in my pipeline
is coming from how I am using the atlas to group together voxels into ROIs, but I am not sure. I have listed my process below with as much detail as possible, if you need any other information let me know:<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black">Link to a matlab figure of granger results:<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><a href="https://drive.google.com/open?id=1CCaTsw8VO0829GJsggBiB0LMquVRx4Ao">https://drive.google.com/open?id=1CCaTsw8VO0829GJsggBiB0LMquVRx4Ao</a><o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><b><u><span style="font-size:12.0pt;color:black">Step 1: Importing headmodel and EEG Data</span></u></b><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black">My first step is loading in the default bem headmodel that comes shipped with fieldtrip, shown below:<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"> <o:p></o:p></span></p>
<p><b><i><span style="font-size:9.0pt;color:black">headmodel = </span></i></b><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<div>
<p class="MsoNormal"><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> struct with fields:</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
<br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> bnd: [1×3 struct]</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> cond: [0.3300 0.0041 0.3300]</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> mat: [3000×3000 double]</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> type: 'dipoli'</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> unit: 'mm'</span></i></b><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black">I then import the EEG data(63 channels, 10-20 electrode layout) and convert the units to mm.
<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black">eegData = eeglab2fieldtrip(EEG,'preprocessing','none');</span></i><i><span style="font-size:12.0pt;color:black"><br>
<br>
</span></i><i><span style="font-size:9.0pt;color:black">eegData.elec = ft_convert_units(header.elec, 'mm');</span></i><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><b><i><span style="font-size:9.0pt;color:black">eegData = </span>
</i></b><b><i><span style="font-size:12.0pt;color:black"><br>
<br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> struct with fields:</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
<br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> elec: [1×1 struct]</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> fsample: 1000</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> trial: {1×113 cell}</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> time: {1×113 cell}</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> label: {1×63 cell}</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> trialinfo: [113×7 table]</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> cfg: [1×1 struct]</span></i></b><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">I then project the electrodes to the scalp using the code below. Plotting afterwards confirms the electrodes are properly aligned with the headmodel.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black">if strcmp(headmodel.type, 'bemcp')</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> scalp_index = 3;</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">elseif strcmp(headmodel.type, 'dipoli')</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> scalp_index = 1;</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">end</span></i><i><span style="font-size:12.0pt;color:black"><br>
<br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg = [];</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.method = 'project'; % onto scalp surface</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.headshape = headmodel.bnd(scalp_index); % scalp surface</span></i><i><span style="font-size:12.0pt;color:black"><br>
<br>
</span></i><i><span style="font-size:9.0pt;color:black">eegData.elec = ft_electroderealign(cfg, eegData.elec);</span></i><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><b><u><span style="font-size:12.0pt;color:black">Step 2: Calculate the foward solution:</span></u></b><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">In this step, I calculate the covariance for my data, and create the source model and calculate the leadfield.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black">cfg = [];</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.covariance = 'yes';</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.covariancewindow = [-inf 0];
</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.keeptrials = 'yes';</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">tlckEeg = ft_timelockanalysis(cfg, eegData);</span></i><i><span style="font-size:12.0pt;color:black"><br>
<br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg = [];</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.headmodel = headmodel;
</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.resolution = 10;</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.inwardshift = 5; </span>
</i><i><span style="font-size:12.0pt;color:black"><br>
<br>
</span></i><i><span style="font-size:9.0pt;color:black">sourcemodel = ft_prepare_sourcemodel(cfg);</span></i><i><span style="font-size:12.0pt;color:black"><br>
<br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg = [];</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.sourcemodel = sourcemodel;
</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.headmodel = headmodel;
</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.elec = tlckEeg.elec;
</span></i><i><span style="font-size:12.0pt;color:black"><br>
<br>
</span></i><i><span style="font-size:9.0pt;color:black">leadfield = ft_prepare_leadfield(cfg);</span></i><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><b><i><span style="font-size:9.0pt;color:black">sourcemodel =
</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
<br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> struct with fields:</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
<br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> dim: [13 18 14]</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> pos: [3276×3 double]</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> unit: 'mm'</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> inside: [3276×1 logical]</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> cfg: [1×1 struct]</span></i></b><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><b><i><span style="font-size:9.0pt;color:black">leadfield = <br>
<br>
struct with fields:<br>
<br>
dim: [13 18 14]<br>
pos: [3276×3 double]<br>
unit: 'mm'<br>
inside: [3276×1 logical]<br>
cfg: [1×1 struct]<br>
leadfield: {1×3276 cell}<br>
label: {63×1 cell}<br>
leadfielddimord: '{pos}_chan_ori'<o:p></o:p></span></i></b></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;color:black"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><b><u><span style="font-size:12.0pt;color:black">Step 3: Calculate the inverse solution</span></u></b><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">In this step, I calculate the sources using eloretta twice, once with the keepfilter option enabled and once with rawtrial enabled(this second run is used to obtain the correct structure format,
the moms calculated from rawtrial are replaced with filter calculated moms). I then take the filters from the first run and multiply them with the original dataset to get the trial by trial mom data, which I use to replace the trial moms that were obtained
with the rawtrial option. Then, for each voxel, I concanate all trial moms and calculate the principal component using svd. Once I have these I recalculate the moms for each trial using only the principal component.
<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black">cfg = [];</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.method = 'eloreta';</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.grid = leadfield;</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.headmodel = headmodel;</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.eloreta.lambda = 0.05;</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.keepmom = 'yes';</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.mne.keepmom = 'yes';</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.eloreta.keepfilter = 'yes';</span></i><i><span style="font-size:12.0pt;color:black"><br>
<br>
</span></i><i><span style="font-size:9.0pt;color:black">sourceEEG = ft_sourceanalysis(cfg,tlckEeg);</span></i><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><b><i><span style="font-size:9.0pt;color:black">sourceEEG = </span>
</i></b><b><i><span style="font-size:12.0pt;color:black"><br>
<br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> struct with fields:</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
<br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> time: [1×4000 double]</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> dim: [13 18 14]</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> inside: [3276×1 logical]</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> pos: [3276×3 double]</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> method: 'average'</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> avg: [1×1 struct]</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> cfg: [1×1 struct]</span></i></b><i><span style="font-size:12.0pt;color:black"><o:p></o:p></span></i></p>
</div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg = [];</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.method = 'eloreta';</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.grid = leadfield;</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.headmodel = headmodel;</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.eloreta.lambda = 0.05;</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.mne.projectnoise = 'yes';</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.keepmom = 'yes';</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.rawtrial = 'yes';</span></i><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black">trialSource = ft_sourceanalysis(cfg,tlckEeg);</span></i><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><i><span style="font-size:12.0pt;color:black"><br>
</span></i><b><i><span style="font-size:9.0pt;color:black">trialSource = </span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
<br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> struct with fields:</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
<br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> time: [1×4000 double]</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> dim: [13 18 14]</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> inside: [3276×1 logical]</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> pos: [3276×3 double]</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> method: 'rawtrial'</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> trial: [1×113 struct]</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> df: 113</span></i></b><b><i><span style="font-size:12.0pt;color:black"><br>
</span></i></b><b><i><span style="font-size:9.0pt;color:black"> cfg: [1×1 struct]</span></i></b><i><span style="font-size:12.0pt;color:black"><o:p></o:p></span></i></p>
</div>
<p class="MsoNormal"><i><span style="font-size:12.0pt;color:black"><br>
<br>
</span></i><i><span style="font-size:9.0pt;color:black">%%</span></i><i><span style="font-size:12.0pt;color:black">
</span></i><i><u><span style="font-size:9.0pt;color:black">Calculating 3 dimensional trial moms</span></u></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">for i = 1:length(sourceEEG.avg.filter)</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> for i2 = 1:length(eegData.trial)</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> if isempty(sourceEEG.avg.filter{i})</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> x = [];</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> else</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> x = sourceEEG.avg.filter{i} * eegData.trial{i2}(:,:);</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> end</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> trialSource.trial(i2).mom{i} = x;</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> end</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">end</span></i><i><span style="font-size:12.0pt;color:black"><br>
<br>
</span></i><i><span style="font-size:9.0pt;color:black">%%</span></i><i><span style="font-size:12.0pt;color:black">
</span></i><i><u><span style="font-size:9.0pt;color:black">Calculating the principal component for each voxel</span></u></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">for i2 = 1:length(trialSource.trial(1).mom)</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> timeseries = [];</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> for i = 1:length(trialSource.trial)</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> timeseries = cat(2,timeseries,trialSource.trial(i).mom{i2});</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> end</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> [u{i2}, s{i2}, v{i2}] = svd(timeseries, 'econ');</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><i><span style="font-size:9.0pt;color:black">end</span></i><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black">%% <u>Calculating 1dimensional trial moms</u></span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">for i = 1:length(sourceEEG.avg.filter)</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> for i2 = 1:length(eegData.trial)</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> if isempty(sourceEEG.avg.filter{i})</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> x = [];</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> else</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black"> x = u{i}(:,1)' *sourceEEG.avg.filter{i} * eegData.trial{i2}(:,:);</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> end</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> trialSource.trial(i2).mom{i} = x;</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> end</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">end</span></i><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><b><u><span style="font-size:12.0pt;color:black">Step 4: Create ROI masks from AAL atlas</span></u></b><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:12.0pt;color:black">In this step I load in the default AAL atlas included with fieldtrip. I then interpolate this atlas onto my sourcemodel. At this point I have tried to use ft_sourceparcellate
to divide up my source data into ROIs, but I receive an error. Both the atlas and my head/source models are volumetric, and because I am using the template headmodel both objects are in MNI space, so I'm not sure how else to troubleshoot this part. Because
of this error, I am using the interpolated atlas to create binary masks and averaging all moms for voxels in each ROI.
<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Code when I try to use ft_sourceparcellate:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black">atlas = ft_read_atlas(broddmanLoc);</span></i><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><b><span style="font-size:9.0pt;color:black">atlas = </span>
</b><b><span style="font-size:12.0pt;color:black"><br>
<br>
</span></b><b><span style="font-size:9.0pt;color:black"> struct with fields:</span></b><b><span style="font-size:12.0pt;color:black"><br>
<br>
</span></b><b><span style="font-size:9.0pt;color:black"> dim: [91 109 91]</span></b><b><span style="font-size:12.0pt;color:black"><br>
</span></b><b><span style="font-size:9.0pt;color:black"> hdr: [1×1 struct]</span></b><b><span style="font-size:12.0pt;color:black"><br>
</span></b><b><span style="font-size:9.0pt;color:black"> transform: [4×4 double]</span></b><b><span style="font-size:12.0pt;color:black"><br>
</span></b><b><span style="font-size:9.0pt;color:black"> unit: 'mm'</span></b><b><span style="font-size:12.0pt;color:black"><br>
</span></b><b><span style="font-size:9.0pt;color:black"> tissue: [91×109×91 double]</span></b><b><span style="font-size:12.0pt;color:black"><br>
</span></b><b><span style="font-size:9.0pt;color:black"> tissuelabel: {1×116 cell}</span></b><b><span style="font-size:12.0pt;color:black"><br>
</span></b><b><span style="font-size:9.0pt;color:black"> coordsys: 'mni'</span></b><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black">cfg = [];</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.method = 'nearest';</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.parameter = 'tissue';</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">atlas2 = ft_sourceinterpolate(cfg,atlas,sourcemodel);</span></i><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><b><i><span style="font-size:9.0pt;color:black">atlas2 = <br>
<br>
struct with fields:<br>
<br>
dim: [13 18 14]<br>
transform: [4×4 double]<br>
unit: 'mm'<br>
inside: [13×18×14 logical]<br>
tissue: [13×18×14 double]<br>
cfg: [1×1 struct]</span></i></b><i><span style="font-size:9.0pt;color:black"><o:p></o:p></span></i></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black"><o:p> </o:p></span></i></p>
</div>
<div>
<p class="MsoNormal"><b><i><span style="font-size:12.0pt;color:black">% Here I try to use the original atlas with ft_sourceparcellate and receive an error</span></i></b><i><span style="font-size:9.0pt;color:black"><o:p></o:p></span></i></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black">cfg = [];<o:p></o:p></span></i></p>
</div>
<div>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black">cfg.method = 'eig';<br>
cfg.parcellation = 'tissue';<b><o:p></o:p></b></span></i></p>
</div>
<div>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black">ft_sourceparcellate(cfg,trialSource,atlas)<o:p></o:p></span></i></p>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black">Error using ft_sourceparcellate (line 109)<br>
the source positions are not consistent with the parcellation, please use FT_SOURCEINTERPOLATE<o:p></o:p></span></i></p>
</div>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black"><o:p> </o:p></span></i></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black">% </span></i><b><i><span style="font-size:12.0pt;color:black">As you can see above, when I interpolate the atlas onto the source model, tissuelabel is missing in atlas2, so it is not recognized
as a parcellation. When I add tissuelabel from atlas to atlas2, another error appears.</span></i></b><i><span style="font-size:9.0pt;color:black"><o:p></o:p></span></i></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black"><o:p> </o:p></span></i></p>
</div>
<div>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black">cfg = [];<br>
cfg.method = 'eig';<br>
cfg.parcellation = 'tissue';<br>
ft_sourceparcellate(cfg,trialSource,atlas2)<br>
Error using ft_sourceparcellate (line 97)<br>
This function requires parcellation data as input, see ft_datatype_parcellation.<o:p></o:p></span></i></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black"><o:p> </o:p></span></i></p>
</div>
<div>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black">atlas2.tissuelabel = atlas.tissuelabel;<o:p></o:p></span></i></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black">cfg = [];<br>
cfg.method = 'eig';<br>
cfg.parcellation = 'tissue';<br>
ft_sourceparcellate(cfg,trialSource,atlas2)<br>
Error using ft_sourceparcellate (line 97)<br>
each index value should have a corresponding entry in "tissuelabel"<o:p></o:p></span></i></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black"><o:p> </o:p></span></i></p>
</div>
<div>
<p class="MsoNormal"><b><i><span style="font-size:12.0pt;color:black">% Because of these errors, I instead create my own binary masks for each ROI, using methods from this tutorial:
</span></i></b><i><span style="font-size:9.0pt;color:black"><o:p></o:p></span></i></p>
</div>
<div>
<p class="MsoNormal"><b><i><span style="font-size:12.0pt;color:black"><a href="http://www.fieldtriptoolbox.org/faq/how_can_i_map_source_locations_between_two_different_representations/">http://www.fieldtriptoolbox.org/faq/how_can_i_map_source_locations_between_two_different_representations/</a></span></i></b><i><span style="font-size:9.0pt;color:black"><o:p></o:p></span></i></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black"><o:p> </o:p></span></i></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black"> atlas = ft_read_atlas(broddmanLoc);</span></i><i><span style="font-size:12.0pt;color:black"><o:p></o:p></span></i></p>
<div>
<p class="MsoNormal"><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg = [];</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.method = 'nearest';</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.parameter = 'tissue';</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">atlas2 = ft_sourceinterpolate(cfg,atlas,sourcemodel);</span></i><i><span style="font-size:12.0pt;color:black"><br>
<br>
</span></i><i><span style="font-size:9.0pt;color:black">roiData.time = eegData.time;</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">roiData.label = atlas.tissuelabel';</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">roiData.trial = {};</span></i><i><span style="font-size:12.0pt;color:black"><br>
<br>
</span></i><i><span style="font-size:9.0pt;color:black">missingLabels = [];</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">for i = 1:length(atlas.tissuelabel)</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> indx = find(atlas2.tissue==i);</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> if isempty(indx)</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> missingLabels = [missingLabels i];</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> end</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> for i3 = 1:length(trialSource.trial)</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> timeseries = [];</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> for i2 = 1:length(indx)</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> try</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> timeseries = cat(1,timeseries,trialSource.trial(i).mom{indx(i2)});</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> end</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> end</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> if ~isempty(timeseries)</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> for i4 = 1:size(timeseries,2)</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> roiData.trial{i3}(i,i4) = mean(timeseries(:,i4));</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> end</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> else</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> roiData.trial{i3}(i,:) = ones(1,length(roiData.time{1}))*10^-10;</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> end</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> end</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black"> </span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">end</span></i><i><span style="font-size:12.0pt;color:black"><o:p></o:p></span></i></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black">Using this method, some ROIs from the atlas have zero indices found in the source model, which is confusing to me. I tried replace the source data for missing ROIs with a very small non-zero #(10^-10) so that the
rest of the script runs. Looking at the indices now I realize that these are the indices with extrememly high granger values, so adding in small non-zero values is not a valid solution it seems. Is there any reason for these ROIs to not be showing up in my
model? The missing indices are listed below. I assume that the issue is coming from the interpolation of the atlas.<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><i><span style="font-size:9.0pt;color:black">missingLabels = [21 70 79 80 95 101 107 108 109]</span></i><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><b><u><span style="font-size:12.0pt;color:black">Step 5: Calculate Connectivity</span></u></b><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black">In this step I calculate granger causality. I don't think anything is going wrong here, after having gone through all of my code for this email I realize that the missing ROIs are the most likely culprit.<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><i><span style="font-size:9.0pt;color:black">cfg = [];</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.output = 'fourier';</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.method = 'mtmfft';</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.foilim = [0 50];</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.tapsmofrq = 4;</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.keeptrials = 'yes';</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.pad = 4;</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">freq = ft_freqanalysis(cfg, roiData);</span></i><i><span style="font-size:12.0pt;color:black"><br>
<br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg = [];</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.method = 'granger';</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">cfg.granger.sfmethod = 'bivariate';</span></i><i><span style="font-size:12.0pt;color:black"><br>
</span></i><i><span style="font-size:9.0pt;color:black">granger = ft_connectivityanalysis(cfg, freq);</span></i><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><b><u><span style="font-size:12.0pt;color:black">Conclusions</span></u></b><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">After going through all of my code, I realize the main issue is that some of the atlas ROIs have no indices in my sourcemodel after interpolating. Is there any fix/advice that you can suggest to
either fix this problem, or to make ft_sourceparcellate work so that I can avoid this issue altogether? I realize there is a lot of code and steps to go through here, and I appreciate any help that you can provide. This mailing list has been a great resource
for me so far, and I hope I can return the favor to some fellow fieldtrippers soon!<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Best,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:12.0pt;color:black">Michael Glassen<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div class="MsoNormal" align="center" style="text-align:center"><span style="font-size:12.0pt;color:black">
<hr size="0" width="100%" align="center">
</span></div>
<div id="divRplyFwdMsg">
<p class="MsoNormal"><b><span style="color:black">From:</span></b><span style="color:black"> fieldtrip <fieldtrip-bounces@science.ru.nl> on behalf of Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen@donders.ru.nl><br>
<b>Sent:</b> Thursday, May 14, 2020 2:02:38 AM<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] Computing source-level ROI EEG connectivity</span><span style="font-size:12.0pt;color:black">
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"> <o:p></o:p></span></p>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Dear Michael, <o:p>
</o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">The convention is left column to right column, so in this case RGAST to LGAST. the stuff between the ‘[‘ is to indicate that the pairwise metric has been obtained with a bivariate model that included
LGAST and RGAST.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Best wishes,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Jan-Mathijs<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><br>
<br>
<o:p></o:p></span></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">On 14 May 2020, at 03:14, Michael Glassen - Biomedical Engineer <<a href="mailto:MGlassen@kesslerfoundation.org">MGlassen@kesslerfoundation.org</a>> wrote:<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<div>
<div id="divtagdefaultwrapper">
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Hi<span class="apple-converted-space"> </span></span><span style="font-size:13.5pt;color:black">Jan-Mathijs</span><span style="font-size:12.0pt;color:black">,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">I implemented all of your suggestions but I had a quick question on the organization of the bivariate granger connectivity structure. From what I can understand, this should compute connectivity
from each channel to every other channel. This is my connectivity structure:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">struct with fields:<br>
<br>
labelcmb: {14762×2 cell}<br>
dimord: 'chancmb_freq'<br>
grangerspctrm: [14762×201 double]<br>
freq: [1×201 double]<br>
cfg: [1×1 struct]<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">And looking at an entry of labelcmb(14762,:) gives:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">1×2 cell array<br>
<br>
{'RGAST[RGAST,LGAST]'} {'LGAST[RGAST,LGAST]'}<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">So does this mean that grangerspctrm(14762,:) is the granger connectivity from RGAST to LGAST, or is it from LGAST to RGAST?<span class="apple-converted-space"> </span><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Best,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Michael Glassen<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
</div>
<div class="MsoNormal" align="center" style="text-align:center"><span style="font-size:12.0pt;color:black">
<hr size="2" width="1094" style="width:820.25pt" align="center">
</span></div>
<div id="divRplyFwdMsg">
<p class="MsoNormal"><b><span style="color:black">From:</span></b><span class="apple-converted-space"><span style="color:black"> </span></span><span style="color:black">fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>>
on behalf of Schoffelen, J.M. (Jan Mathijs) <<a href="mailto:jan.schoffelen@donders.ru.nl">jan.schoffelen@donders.ru.nl</a>><br>
<b>Sent:</b><span class="apple-converted-space"> </span>Saturday, May 9, 2020 4:11:51 AM<br>
<b>To:</b><span class="apple-converted-space"> </span>FieldTrip discussion list<br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: [FieldTrip] Computing source-level ROI EEG connectivity</span><span style="font-size:10.5pt;font-family:Helvetica;color:black">
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"> <o:p></o:p></span></p>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:Helvetica;color:black">Hi Wanze,</span><span style="font-size:10.5pt;font-family:Helvetica;color:black">
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<div>
<div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:Helvetica;color:black">I have two short questions regarding your suggestions to Michael: 1) any reason for why doing svd for concatenated trials would work better than doing svd per trial? </span><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p></o:p></span></p>
</div>
</div>
</div>
</blockquote>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:Helvetica;color:black">Well, it’s not that ‘it works better’, but using a per trial svd will result in a different orientation estimate per trial, which then inherently assumes a source model that
fixes the location of the dipole, but not its orientation.</span><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:Helvetica;color:black"><br>
<br>
</span><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p></o:p></span></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:Helvetica;color:black">2) If we do svd with concatenated trials do we need to re-segment the data into epochs/trials? I think ft_freqanalysis and ft_connectivity would work way more efficiently
if they are applied to data in epochs rather than one long trial, although I am not 100% assured. </span><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p></o:p></span></p>
</div>
</div>
</div>
</blockquote>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:Helvetica;color:black">Indeed, in most situations (particularly if the experimental protocol is epoch based) it is mandatory to maintain the epoch-structure in the spectral decomposition and connectivity
estimation step. To this end the concatenation step is an intermediate one, used only to compute the principal orientation, and this orientation can then be applied to the data structure that still contains the epochs, either using a for-loop across the individual
epochs, or exploiting the external/cellfunction code, by a direct multiplication.</span><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:Helvetica;color:black">Best wishes,</span><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:Helvetica;color:black">Jan-Mathijs</span><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
</div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><br>
<br>
<o:p></o:p></span></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:Helvetica;color:black">Look forward to hearing from you. </span><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:Helvetica;color:black">Best,</span><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:Helvetica;color:black">Wanze</span><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black">Schoffelen, J.M. (Jan Mathijs) <<a href="mailto:jan.schoffelen@donders.ru.nl" target="_blank">jan.schoffelen@donders.ru.nl</a>></span><span lang="EN-GB" style="font-size:10.5pt;font-family:"MS Mincho";color:black">于</span><span style="font-size:10.5pt;font-family:Helvetica;color:black">2020</span><span lang="EN-GB" style="font-size:10.5pt;font-family:"MS Mincho";color:black">年</span><span style="font-size:10.5pt;font-family:Helvetica;color:black">5</span><span lang="EN-GB" style="font-size:10.5pt;font-family:"MS Mincho";color:black">月</span><span style="font-size:10.5pt;font-family:Helvetica;color:black">8</span><span lang="EN-GB" style="font-size:10.5pt;font-family:"MS Mincho";color:black">日</span><span lang="EN-GB" style="font-size:10.5pt;font-family:Helvetica;color:black">
</span><span lang="EN-GB" style="font-size:10.5pt;font-family:"MS Mincho";color:black">周五上午</span><span style="font-size:10.5pt;font-family:Helvetica;color:black">10:35</span><span lang="EN-GB" style="font-size:10.5pt;font-family:"MS Mincho";color:black">写道：</span><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p></o:p></span></p>
</div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm">
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black">Hi Michael,
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black">The WFU atlas is a volumetrically defined atlas, correct? So, in order for the parcellation to work, the atlas needs to be mapped onto the cortically constrained sheet of
dipoles that you used for source reconstruction.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black">This is not entirely trivial, but doable. If you obtained your atlas already as represented on a cortically constrained set of locations, then you need to ensure that these
locations topologically map to the dipole locations of your source model. <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black">Best wishes,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black">Jan-Mathijs<o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><br>
<br>
<o:p></o:p></span></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black">On 8 May 2020, at 16:15, Michael Glassen - Biomedical Engineer <<a href="mailto:MGlassen@kesslerfoundation.org" target="_blank">MGlassen@kesslerfoundation.org</a>> wrote:<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black">Thank you everyone for the help!<br>
<br>
Just one final question, I got the Brodmann area atlas and the hemisphere atlas from this toolbox SPM “WFU-PickAtlas”.<br>
<br>
Does anyone know if there is a Brodmann area atlas that is known to work with fieldtrip?<br>
<br>
Best,<br>
Michael Glassen<span class="apple-converted-space"> </span> <o:p></o:p></span></p>
<div class="MsoNormal" align="center" style="text-align:center"><span style="font-size:10.5pt;font-family:Helvetica;color:black">
<hr size="2" width="1060" style="width:795.15pt" align="center">
</span></div>
<div id="m_-9057387112358115007m_-3568020509046707828divRplyFwdMsg">
<p class="MsoNormal"><b><span style="color:black">From:</span></b><span class="apple-converted-space"><span style="color:black"> </span></span><span style="color:black">fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank">fieldtrip-bounces@science.ru.nl</a>>
on behalf of Schoffelen, J.M. (Jan Mathijs) <<a href="mailto:jan.schoffelen@donders.ru.nl" target="_blank">jan.schoffelen@donders.ru.nl</a>><br>
<b>Sent:</b><span class="apple-converted-space"> </span>Friday, May 8, 2020 3:17:56 AM<br>
<b>To:</b><span class="apple-converted-space"> </span>FieldTrip discussion list<br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: [FieldTrip] Computing source-level ROI EEG connectivity</span><span style="font-size:10.5pt;font-family:Helvetica;color:black">
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"> <o:p></o:p></span></p>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black">Hi Michael,
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black">Adding to Wanze’s and Xavier’s replies:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
<div>
<div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<div>
<p class="MsoNormal"><span style="color:#1F497D"> I went through and plotted a couple different time series from the mom field from different trials and the same dipole, they are not equal and the shape looks ok to me, the magnitudes range from
10^-7 to 10^-4, is that normal? Source was calculated with everything in meters if that matters. Can you explain a little more the other method for calculating mom? The only option I have to add is keepfilter to sourceanalysis? And then I multiply each of
these filters against the trial data matrix and it will leave me with what rawtrial is giving me but more reliably? Can I then still use the parcellate option on the output here? Or is this not necessary as rawtrial seems to be working?</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
</div>
</blockquote>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black">If ‘rawtrial’ works, than this would be fine. I was a bit worried (and I’d need to look in the code myself in some more detail) because historically the ‘rawtrial’-functionality
was implemented for the beamformer algorithms, and not for the MNE. As such, it has never been tested thoroughly for MNE, so although it seems to produce an output for you, I am not 100% sure that it’s correct. Also, anecdotally, the ‘rawtrial’/’singletrial’
functionality for the beamformers is shaky in itself, and we still have it on our to-do-list to make the code more internally consistent and correct. <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><br>
<br>
<o:p></o:p></span></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">-In order to get a ‘parcellated’ representation of your source level data, I recommend to use ft_sourceparcellate, which should achieve the parcellation you
performed by hand (with the binary masks).</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> </span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="color:black"> </span></i><span style="color:#1F4E79">I tried using the ft_sourceparcellate function but I was running into a memory issue when ran on the rawtrial source, and when I remove that option and run
it on the default trial-averaged sources I get a different error, which is pasted below. mri2 is the broddman area atlas interpolated onto my source model. Also, is there any way to parcellate twice with the function like I am doing by hand? The broddman area
atlas I have is not divided into left and right hemispheres so I have another atlas I am using that is divided into hemispheres.</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:36.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">mri2 =</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> </span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> struct with fields:</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> </span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> pos: [8196×3 double]</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> tri: [16384×3 double]</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> unit: 'm'</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> tissue: [8196×1 double]</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> tissuelabel: {1×70 cell}</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> cfg: [1×1 struct]</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> </span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> cfg =</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> </span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> struct with fields:</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> </span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> method: 'mean'</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> parcellation: 'tissue'</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> parameter: 'mom'</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> </span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">ft_sourceparcellate(cfg,sourceEEG,mri2)</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">there is no "Dentate" in "tissue"</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">there is no "Hypothalamus" in "tissue"</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">there is no "Substania Nigra" in "tissue"</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">there is no "Caudate Tail" in "tissue"</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">there is no "Putamen" in "tissue"</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">there is no "Medial Geniculum Body" in "tissue"</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">there is no "Lateral Globus Pallidus" in "tissue"</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">there is no "Subthalamic Nucleus" in "tissue"</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">there is no "Medial Globus Pallidus" in "tissue"</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">there is no "Lateral Geniculum Body" in "tissue"</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">there is no "Anterior Commissure" in "tissue"</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">there is no "Ventral Posterior Lateral Nucleus" in "tissue"</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">there is no "Ventral Posterior Medial Nucleus" in "tissue"</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">there is no "Ventral Lateral Nucleus" in "tissue"</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">there is no "Ventral Anterior Nucleus" in "tissue"</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">there is no "Caudate Body" in "tissue"</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">there is no "Lateral Posterior Nucleus" in "tissue"</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:108.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">there is no "Lateral Dorsal Nucleus" in "tissue"</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:36.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">there is no "Midline Nucleus" in "tissue"</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">there are in total 8196 positions, 8190 positions are inside the brain, 2611 positions have a label</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">2609 of the positions inside the brain have a label</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">2609 of the labeled positions are inside the brain</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">5581 of the positions inside the brain do not have a label</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">creating 70 parcels for parameter mom by taking the mean</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">computing parcellation</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">Index exceeds the number of array elements (0).</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> </span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">Error in ft_sourceparcellate>cellmean1 (line 488)</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">y = x{1};</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> </span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div style="margin-left:72.0pt">
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">Error in ft_sourceparcellate (line 226)</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black"> tmp(j,:,:) = cellmean1(dat(seg==j));</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:#1F4E79"> -If I cannot get source parcellate to work, does my method of creating a mask and pulling out the source powers seem sound? I see that I should use mom instead of pow, so would I then just take
all the voxels in an ROI and average the x direction together, the y direction together and the z together? Then find the direction with the largest power and use that as my 1by x time series power(using svd as described in documentation)? This is what I’m
assuming sourceparcellate does if I select ‘eig’ as the method.</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
</blockquote>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black">-With regard to thte parcellation: understood if memory limitations prevent you from using it. Yet, the error message you get when using the trial-averaged data suggests an
issue with your atlas. Where did you get it from? It looks as if only 2611 out of the 8196 cortical locations have a label. Is that according to your expectations? <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black">-If indeed you are to manually parcellate (with the mask), you can do one of the following:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"> * average x/y/z across dipole locations, followed by an svd (I’d recommend to do this svd on the trial-concatenated data, rather than on a per-trial basis)<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"> * (to mimick the ‘eig’ method): concatenate the time series across dipole locations (and trials), followed by a single svd on the whole matrix.<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><br>
<br>
<o:p></o:p></span></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black">ALSO IMPORTANT: if you go for a granger-like measure (granger/dtf/pdc), in the spectral analysis you should probably use a decent amount of zero padding (cfg.pad)
and sufficient tapsmofrq in order to get spectral data that stands a chance to get a stable factorization.</span></i><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:#1F497D"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:#1F497D"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:#1F497D"> -Finally, if I choose to go for granger, what kind of cfg.pad and tapsmofrq would you recommend? I am mostly interested in the beta band(12-30Hz) and my trial lengths are 357 samples(1.3 seconds)</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
</blockquote>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black">Irrespective of using granger or the disrecommended dtf/pdc, all techniques that require a spectral factorization need padding and smoothing. In your case I’d recommend a
padding of 4 (cfg.pad = 4), and a cfg.tapsmofrq somewhere in the range of 3 and 6 (but the latter is a bit of ‘wet finger work’, as we sould say in Dutch -> google for ’natte vingerwerk’ if you want to learn more).<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black">Best wishes,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black">Jan-Mathijs<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><br>
<br>
<o:p></o:p></span></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<div>
<p class="MsoNormal"><b><span style="color:black">Subject:</span></b><span style="color:black"> Re: [FieldTrip] Computing source-level ROI EEG connectivity</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black">Dear Michael, </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"> <o:p></o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black">It looks that you already got quite far! I agree that the DTF values do not make much sense.</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"> <o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black">a few pointers:</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"> <o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black">-I would use some regularisation for the MNE reconstruction.</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black">-I would check whether the individual trials after source reconstruction yield meaningful values in the ‘mom’-field. Particularly, are the different trials different?
Do the time series look meaningful to begin with (both in terms of signal magnitude and ’shape’)? The reason I ask, is that I am not fully sure whether the ‘rawtrial’ option is behaving according to your expectations.</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black">-Another way for getting the mom would be to use cfg.keepfilter in ft_sourceanalysis, and left-multiply each dipole location’s ’spatial filter’ (in sourceEEG.avg.filter)
with a dataEEG.trial matrix.</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black">-IMPORTANT: don’t use the ‘pow’ for the subsequent spectral analysis and connectivity estimation. You should work with the mom.</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black">-In order to get a ‘parcellated’ representation of your source level data, I recommend to use ft_sourceparcellate, which should achieve the parcellation you
performed by hand (with the binary masks).</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black">-The parcellation operation can be an average of the mom across the dipoles that belong to a parcel, but an alternative might be the the 1st principal component.
The advantage of the latter would be that the per-parcel signal will be reduced to a single time series (rather then 3 x/y/z orientation time courses), which is convenient (and required) for the interpretation of the subsequent computations.</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black">-You may want to think a bit about the depth weighting, since the MNE favors superficial locations in terms of amplitude, and this will also percolate to the
way the parcellated time series are computed.</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black">-IMPORTANT: using ‘dtf’ without any additional specification of parameters is probably not what you want here. The reason is that under the hood a multivariate
factorization of the spectral matrix is performed (at least: an attempt is made), which will miserably fail in your case. The reason for this failure (thinking a bit more about this, I am quite surprised that it worked to begin with) is the fact that you ask
for a factorization of a size NparcelxNparcel(xfrequency bins) matrix, where the effective rank of the matrix is less than the number of channels in your EEG array. Even if Nparcel is less than the number of EEG electrodes, this factorization will be very
poorly estimated and nonsensical. I’d recommend using ‘granger’ as a method, in combination with cfg.granger.sfmethod = ‘bivariate’. This results in a parcel-pairwise factorization (which is hopefully stable most of the time). I am not a fan of dtf/pdc anyway
given that the measures are claimed to provide estimates unproblematic estimates that are interpretable without any caveats.</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black">-ALSO IMPORTANT: if you go for a granger-like measure (granger/dtf/pdc), in the spectral analysis you should probably use a decent amount of zero padding (cfg.pad)
and sufficient tapsmofrq in order to get spectral data that stands a chance to get a stable factorization.</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"> <o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black">So, no definitive answers unfortunately, but perhaps some food for thought that might get you closer to a good result.</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"> <o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black">Good luck and keep up the good work,</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"> <o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black">Jan-Mathijs</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"> <o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"> <o:p></o:p></span></p>
</div>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"> <o:p></o:p></span></p>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black">J.M.Schoffelen, MD PhD<br>
Associate PI, VIDI-fellow - PI, language in interaction<br>
Telephone: +31-24-3614793</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black">Physical location: room 00.028</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black">Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"> <o:p></o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p> </o:p></span></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black">On 6 May 2020, at 22:34, Michael Glassen - Biomedical Engineer <<a href="mailto:MGlassen@kesslerfoundation.org" target="_blank"><span style="color:purple">MGlassen@kesslerfoundation.org</span></a>>
wrote:<o:p></o:p></span></p>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="color:black">Hi all,</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="color:black">I am having issues using fieldtrip for source reconstruction and connectivity analysis with preprocessed EEG data. I believe the issue is occurring when I try to
project my sources to specific ROIs before getting the connectivity. I have outlined my pipeline below:</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="color:black">-Because I do not have subject MRIs, I am using a template headmodel and sourcemodel that come included with fieldtrip</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="color:black"> - headmodel = standard_bem.mat</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="color:black"> -sourcemodel = cortex_8196.surf.gii</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="color:black">-After importing EEG data, I project the EEG electrodes to the scalp using the code below:</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> </span><span style="font-size:9.0pt;font-family:"Courier New";color:blue">if</span><span style="font-size:9.0pt;font-family:"Courier New";color:black"> strcmp(headmodel.type, </span><span style="font-size:9.0pt;font-family:"Courier New";color:#A020F0">'bemcp'</span><span style="font-size:9.0pt;font-family:"Courier New";color:black">)</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Courier New";color:black"> scalp_index = 3;</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:blue">elseif</span><span style="font-size:9.0pt;font-family:"Courier New";color:black"> strcmp(headmodel.type, </span><span style="font-size:9.0pt;font-family:"Courier New";color:#A020F0">'dipoli'</span><span style="font-size:9.0pt;font-family:"Courier New";color:black">)</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Courier New";color:black"> scalp_index = 1;</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:blue">end</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg = [];</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.method = </span><span style="font-size:9.0pt;font-family:"Courier New";color:#A020F0">'project'</span><span style="font-size:9.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.headshape = headmodel.bnd(scalp_index);</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Courier New";color:forestgreen"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">eegData.elec = ft_electroderealign(cfg, eegData.elec);</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black">-I then calculate covariance on a trial basis and calculate the leadfield matrix:</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> </span><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg = [];</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.covariance = </span><span style="font-size:9.0pt;font-family:"Courier New";color:#A020F0">'yes'</span><span style="font-size:9.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.covariancewindow = [-inf 0];</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.keeptrials = </span><span style="font-size:9.0pt;font-family:"Courier New";color:#A020F0">'yes'</span><span style="font-size:9.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">tlckEeg = ft_timelockanalysis(cfg, eegData);</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg = [];</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.elec = tlckEeg.elec; </span><span style="font-size:9.0pt;font-family:"Courier New";color:forestgreen">% sensor information</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.channel = tlckEeg.label; </span><span style="font-size:9.0pt;font-family:"Courier New";color:forestgreen">% the used channels</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.grid = sourcemodel; </span><span style="font-size:9.0pt;font-family:"Courier New";color:forestgreen">% source points</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.headmodel = headmodel; </span><span style="font-size:9.0pt;font-family:"Courier New";color:forestgreen">% volume conduction model</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.singleshell.batchsize = 5000; </span><span style="font-size:9.0pt;font-family:"Courier New";color:forestgreen">% speeds up the computation</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">leadfield = ft_prepare_leadfield(cfg);</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black">-Now with the leadfield calculated, I calculate sources on a trial basis here:</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg = [];</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.method = </span><span style="font-size:9.0pt;font-family:"Courier New";color:#A020F0">'mne'</span><span style="font-size:9.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.sourcemodel = leadfield;</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.headmodel = headmodel;</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.mne.prewhiten = </span><span style="font-size:9.0pt;font-family:"Courier New";color:#A020F0">'yes'</span><span style="font-size:9.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.mne.lambda = 0;</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.mne.scalesourcecov = </span><span style="font-size:9.0pt;font-family:"Courier New";color:#A020F0">'yes'</span><span style="font-size:9.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.rawtrial = </span><span style="font-size:9.0pt;font-family:"Courier New";color:#A020F0">'yes'</span><span style="font-size:9.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">sourceEEG = ft_sourceanalysis(cfg,tlckEeg);</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> sourceEEG = </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> struct with fields:</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> time: [1×357 double]</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> inside: [8196×1 logical]</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> pos: [8196×3 double]</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> tri: [16384×3 double]</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> method: 'rawtrial'</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> trial: [1×400 struct]</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> df: 400</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> cfg: [1×1 struct]</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> sourceEEG.trial = </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> 1×400 struct array with fields:</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> mom</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> pow</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> noisecov</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="color:black">size(sourceEEG.trial(1).pow)</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div style="margin-left:36.0pt">
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="color:black">ans =</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> 8196 357</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="color:black">-So at this point I have 400 trials, and for each of these trials I have a time course of source power at 8196 voxels and 357 time points for each of those voxels.</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="color:black">-I then import two atlases, one that includes broddman areas and one that includes left and right hemispheres. I interpolate these atlases onto my source model and
get the following:</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="color:black"> </span><span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:black">broddman =</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:8.0pt;margin-left:36.0pt;text-indent:36.0pt;line-height:11.65pt">
<span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:black">struct with fields:</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:black"> pos: [8196×3 double]</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:black"> tri: [16384×3 double]</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:black"> unit: 'm'</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:black"> tissue: [8196×1 double] (<b>each of these is a value 1-70, corresponding
to which atlas entry the voxel is located in)</b></span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:black"> tissuelabel: {1×70 cell}<b>(ROI labels for the atlas, includes broddman
areas not separated by hemisphere)</b></span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:black"> cfg: [1×1 struct]</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;text-indent:36.0pt;line-height:11.65pt">
<span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:black">hemis2 =</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:8.0pt;margin-left:36.0pt;text-indent:36.0pt;line-height:11.65pt">
<span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:black">struct with fields:</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:8.0pt;margin-left:36.0pt;text-indent:36.0pt;line-height:11.65pt">
<span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:black">pos: [8196×3 double]</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:black"> tri: [16384×3 double]</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:black"> unit: 'm'</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:black"> tissue: [8196×1 double] (<b>each of these is a value 1-7, corresponding
to which atlas entry the voxel is located in)</b></span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:black"> tissuelabel: {1×7 cell} <b>(ROI Labels for hemisphere atlas, contains
3 Left areas, 3 Right Areas and one inter-hemispheric)</b></span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:black"> cfg: [1×1 struct]</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="font-size:9.0pt;font-family:"Calibri Light",sans-serif;color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="color:black">Now I create a binary mask for each left and right broddman area. For each ROI in the broddman area atlas(1-70), I find all voxels that are located within. This gives
me a list of voxels for each broddman area. I then take each of these lists and find which are in the left hemisphere and which are in the right to get left and right broddman areas.</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="color:black">After these steps I am left with 140 binary masks, (size 1x8196), which equal 1 if the voxel is contained in the specific ROI and 0 if it is not. Using these masks,
I extract the time course power for each ROI by taking the mean power of every voxel in the roi at each time point:</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;color:black"> </span><span style="font-size:9.0pt;font-family:"Courier New";color:black">roiData(i,i3,i2) = mean(sourceEEG.trial(i2).pow(Masks{i},i3));</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Courier New";color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">where i = roi number,</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Courier New";color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Courier New";color:black"> i2 = trial number,</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Courier New";color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Courier New";color:black"> i3 = time point</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Courier New";color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black">In order to get this data into fieldtrip format, I put ROI data into an EEGLAB structure along with 6 emg channels that were recorded at the same time and use eeglab2fieldtrip function to have a fieldtrip structure
containing the broddman area sources as channels. (contained in <i>header</i>)</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black">After this I perform the final step of computing dtf connectivity between each of the source rois and the emg channels with the code below:</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg = [];</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.method = </span><span style="font-size:9.0pt;font-family:"Courier New";color:#A020F0">'mtmfft'</span><span style="font-size:9.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.taper = </span><span style="font-size:9.0pt;font-family:"Courier New";color:#A020F0">'dpss'</span><span style="font-size:9.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.output = </span><span style="font-size:9.0pt;font-family:"Courier New";color:#A020F0">'fourier'</span><span style="font-size:9.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.tapsmofrq = 2;</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">freq = ft_freqanalysis(cfg, header);</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg = [];</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.method = </span><span style="font-size:9.0pt;font-family:"Courier New";color:#A020F0">'dtf'</span><span style="font-size:9.0pt;font-family:"Courier New";color:black">;</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black">dtf = ft_connectivityanalysis(cfg, freq);</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New";color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black">The values I get in DTF are extremely low, 10^-20. I am not sure why but I believe it has to do with the way I am projecting source activations onto specific ROIs. Any help or advice on how to change my pipeline
is appreciated.</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black">Best,</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span style="color:black">Michael Glassen</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="font-size:9.0pt;color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.65pt"><span style="color:black"> </span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><br>
_______________________________________________<br>
fieldtrip mailing list<br>
</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank"><span style="font-size:10.5pt;font-family:Helvetica;color:#954F72">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</span></a></span><span style="font-size:10.5pt;font-family:Helvetica;color:black"><br>
</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><a href="https://doi.org/10.1371/journal.pcbi.1002202" target="_blank"><span style="font-size:10.5pt;font-family:Helvetica;color:#954F72">https://doi.org/10.1371/journal.pcbi.1002202</span></a><o:p></o:p></span></p>
</div>
</div>
</blockquote>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"> <o:p></o:p></span></p>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"> <o:p></o:p></span></p>
</div>
</div>
</div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><br>
_______________________________________________<br>
fieldtrip mailing list<br>
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
<a href="https://doi.org/10.1371/journal.pcbi.1002202" target="_blank">https://doi.org/10.1371/journal.pcbi.1002202</a><o:p></o:p></span></p>
</blockquote>
</div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
</div>
</div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><br>
<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black">_______________________________________________<br>
fieldtrip mailing list<br>
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
<a href="https://doi.org/10.1371/journal.pcbi.1002202" target="_blank">https://doi.org/10.1371/journal.pcbi.1002202</a><o:p></o:p></span></p>
</div>
</blockquote>
</div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
</div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black">_______________________________________________<br>
fieldtrip mailing list<br>
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
<a href="https://doi.org/10.1371/journal.pcbi.1002202" target="_blank">https://doi.org/10.1371/journal.pcbi.1002202</a><o:p></o:p></span></p>
</blockquote>
</div>
</div>
</div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black">_______________________________________________<br>
fieldtrip mailing list<br>
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
<a href="https://doi.org/10.1371/journal.pcbi.1002202">https://doi.org/10.1371/journal.pcbi.1002202</a><o:p></o:p></span></p>
</div>
</blockquote>
</div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><o:p> </o:p></span></p>
</div>
</div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica;color:black"><br>
<span class="apple-converted-space"> </span>_______________________________________________<br>
fieldtrip mailing list<br>
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
<a href="https://doi.org/10.1371/journal.pcbi.1002202">https://doi.org/10.1371/journal.pcbi.1002202</a></span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
</blockquote>
</div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
</div>
</div>
</div>
</div>
</body>
</html>