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<p class="MsoNormal">Hi all,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">-Because I do not have subject MRIs, I am using a template headmodel and sourcemodel that come included with fieldtrip<o:p></o:p></p>
<p class="MsoNormal"> - headmodel = standard_bem.mat<o:p></o:p></p>
<p class="MsoNormal"> -sourcemodel = cortex_8196.surf.gii<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">-After importing EEG data, I project the EEG electrodes to the scalp using the code below:<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<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:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black"> scalp_index = 3;</span><span style="font-size:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<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:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black"> scalp_index = 1;</span><span style="font-size:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:blue">end</span><span style="font-size:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:blue"></span><span style="font-size:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg = [];</span><span style="font-size:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<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">;
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.headshape = headmodel.bnd(scalp_index);
</span><span style="font-size:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:forestgreen"> </span><span style="font-size:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">eegData.elec = ft_electroderealign(cfg, eegData.elec);<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
-I then calculate covariance on a trial basis and calculate the leadfield matrix:<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">
cfg = [];</span><span style="font-size:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<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:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.covariancewindow = [-inf 0];
</span><span style="font-size:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<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:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">tlckEeg = ft_timelockanalysis(cfg, eegData);</span><span style="font-size:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black"></span><span style="font-size:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg = [];</span><span style="font-size:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<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:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<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:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<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:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<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:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<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:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">leadfield = ft_prepare_leadfield(cfg);</span><span style="font-size:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
-Now with the leadfield calculated, I calculate sources on a trial basis here:<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg = [];</span><span style="font-size:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<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:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.sourcemodel = leadfield;</span><span style="font-size:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<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""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<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:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.mne.lambda = 0;</span><span style="font-size:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<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:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<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:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">sourceEEG = ft_sourceanalysis(cfg,tlckEeg);</span><span style="font-size:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
sourceEEG = <o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
struct with fields:<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
time: [1×357 double]<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
inside: [8196×1 logical]<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
pos: [8196×3 double]<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
tri: [16384×3 double]<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
method: 'rawtrial'<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
trial: [1×400 struct]<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
df: 400<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
cfg: [1×1 struct]<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
sourceEEG.trial = <o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
1×400 struct array with fields:<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
mom<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
pow<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
noisecov<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
size(sourceEEG.trial(1).pow)<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<o:p> </o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:0in;margin-left:.5in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
ans =<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
8196 357<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">-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.<o:p></o:p></p>
<p class="MsoNormal">-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:<o:p></o:p></p>
<p class="MsoNormal"> <span style="font-size:9.0pt;line-height:106%;font-family:"Calibri Light",sans-serif">
broddman =<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in;text-indent:.5in"><span style="font-size:9.0pt;line-height:106%;font-family:"Calibri Light",sans-serif">struct with fields:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:106%;font-family:"Calibri Light",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:106%;font-family:"Calibri Light",sans-serif"> pos: [8196×3 double]<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:106%;font-family:"Calibri Light",sans-serif"> tri: [16384×3 double]<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:106%;font-family:"Calibri Light",sans-serif"> unit: 'm'<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:106%;font-family:"Calibri Light",sans-serif"> tissue: [8196×1 double] (<b>each of these is a value 1-70, corresponding to which atlas entry the voxel is located
in)<o:p></o:p></b></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:106%;font-family:"Calibri Light",sans-serif"> tissuelabel: {1×70 cell}<b>(ROI labels for the atlas, includes broddman areas not separated by hemisphere)<o:p></o:p></b></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:106%;font-family:"Calibri Light",sans-serif"> cfg: [1×1 struct]<o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:.5in"><span style="font-size:9.0pt;line-height:106%;font-family:"Calibri Light",sans-serif">hemis2 =<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in;text-indent:.5in"><span style="font-size:9.0pt;line-height:106%;font-family:"Calibri Light",sans-serif">struct with fields:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:.5in;text-indent:.5in"><span style="font-size:9.0pt;line-height:106%;font-family:"Calibri Light",sans-serif">pos: [8196×3 double]<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:106%;font-family:"Calibri Light",sans-serif"> tri: [16384×3 double]<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:106%;font-family:"Calibri Light",sans-serif"> unit: 'm'<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:106%;font-family:"Calibri Light",sans-serif"> tissue: [8196×1 double] (<b>each of these is a value 1-7, corresponding to which atlas entry the voxel is located
in)<o:p></o:p></b></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:106%;font-family:"Calibri Light",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:106%;font-family:"Calibri Light",sans-serif"> tissuelabel: {1×7 cell}
<b>(ROI Labels for hemisphere atlas, contains 3 Left areas, 3 Right Areas and one inter-hemispheric)<o:p></o:p></b></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:106%;font-family:"Calibri Light",sans-serif"> cfg: [1×1 struct]<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:106%;font-family:"Calibri Light",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:106%;font-family:"Calibri Light",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal">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.
<o:p></o:p></p>
<p class="MsoNormal">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 style="font-size:9.0pt;line-height:106%"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt"> </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));<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">where i = roi number,<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New""> i2 = trial number,<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New""> <o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New""> i3 = time point<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
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>)<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
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:<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<span style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg = [];</span><span style="font-size:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<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:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<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:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<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:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.tapsmofrq = 2;</span><span style="font-size:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">freq = ft_freqanalysis(cfg, header);</span><span style="font-size:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg = [];</span><span style="font-size:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<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:9.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">dtf = ft_connectivityanalysis(cfg, freq);<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;text-indent:.5in;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt;font-family:"Courier New";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<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.<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
<span style="font-size:9.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
Best,<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:normal;text-autospace:none">
Michael Glassen<o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:106%"><o:p> </o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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