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<div style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
Hi all,</div>
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I have a pipeline working to get source data into trial by trial form, interpolated onto the brainetome atlas using ft_virtual_channel. I was previously taking this data and running connectivity analysis outside of fieldtrip, but I want to run source power
analysis and connectivity analysis in fieldtrip now. The connectivity analysis seems to be straightforward, but as I was trying to follow this tutorial(<a href="https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/example/source_statistics/__;!!HJOPV4FYYWzcc1jazlU!8NKHjd2nuO01v9keAIF1QkHk0sbso2-hl8vMMB6nGjuogzDUXWGBsf9c6DhnkJR5YuewKW4EtUMJR6ctlQ1XD391dPVp$" class="ContentPasted0" id="LPlnk474016">Source
statistics - FieldTrip toolbox</a>), I noticed it required trial by trial source data on the whole brain(not parcellated using an atlas). sourcestatistics can take an atlas in cfg and parcellate for you, but I dont see an option to enter virtual channel data
as an input. </div>
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I tried to use ft_virtualchannel without the atlas in order to get trial by trial data on the whole brain, but received the error message:</div>
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<div class="rtcContent" style="padding:30px"><span class="lineNode" style="font-size:10pt;font-family:Menlo, Monaco, Consolas, "Courier New", monospace;font-weight:normal"><span><span class="ContentPasted2">cfg = [];</span></span></span>
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<span><span class="ContentPasted2">cfg.pos = source_allexp.pos;</span></span></div>
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<span><span class="ContentPasted2">cfg.method = </span><span style="color: rgb(167, 9, 245);" class="ContentPasted2">'svd'</span><span class="ContentPasted2">;</span></span></div>
<span class="lineNode" style="font-size:10pt;font-family:Menlo, Monaco, Consolas, "Courier New", monospace;font-weight:normal"><span><span class="ContentPasted2">roiData = ft_virtualchannel(cfg,timelock_allexp_all,source_allexp);</span></span></span>
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the spatial filter information is missing
<div class="ContentPasted1">for dipole with position [-68 -104 -52].</div>
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<div class="ContentPasted1">Any help in either getting trial based source data for the whole brain working that sourcestatistics can accept as input, or getting sourcestatistics to accept my already parcellated atlas activity would be hugely appreciated. </div>
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<div class="ContentPasted1">I am using the template standard bem headmodel and the template brainnetom atlas <span style="font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-size: 13.3333px; display: inline !important; color: rgb(167, 9, 245); background-color: rgb(255, 255, 255);" class="ContentPasted5">BNA_MPM_thr25_1.25mm.nii</span>
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<div class="ContentPasted1">Best,</div>
<div class="ContentPasted1">Michael Glassen</div>
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<div class="ContentPasted1">%% Code</div>
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<span><span class="ContentPasted3">cfg = [];</span></span></div>
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<span><span class="ContentPasted3">cfg.method = </span><span style="color: rgb(167, 9, 245);" class="ContentPasted3">'project'</span><span class="ContentPasted3">;
</span><span style="color: rgb(0, 128, 19);" class="ContentPasted3">% onto scalp surface</span></span></div>
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<span><span class="ContentPasted3">cfg.headshape = headmodel.bnd(scalp_index); </span>
<span style="color: rgb(0, 128, 19);" class="ContentPasted3">% scalp surface</span></span></div>
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<span><span class="ContentPasted3">eegData.elec = ft_electroderealign(cfg, eegData.elec);</span></span></div>
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<span><span class="ContentPasted3">cfg = [];</span></span></div>
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<span><span class="ContentPasted3">cfg.headmodel = headmodel;</span></span></div>
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<span><span class="ContentPasted3">cfg.elec = eegData.elec;</span></span></div>
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<span><span class="ContentPasted3">cfg.grid.resolution = 4;</span></span></div>
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<span><span class="ContentPasted3">cfg.grid.unit = </span><span style="color: rgb(167, 9, 245);" class="ContentPasted3">'mm'</span><span class="ContentPasted3">;</span></span></div>
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<span><span class="ContentPasted3">cfg.channel = </span><span style="color: rgb(167, 9, 245);" class="ContentPasted3">'all'</span><span class="ContentPasted3">;</span></span></div>
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<span><span class="ContentPasted3">grid = ft_prepare_leadfield(cfg);</span></span></div>
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<span><span class="ContentPasted3">cfg = [];</span></span></div>
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<span><span class="ContentPasted3">cfg.covariance = </span><span style="color: rgb(167, 9, 245);" class="ContentPasted3">'yes'</span><span class="ContentPasted3">;</span></span></div>
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<span><span class="ContentPasted3">cfg.covariancewindow = </span><span style="color: rgb(167, 9, 245);" class="ContentPasted3">'all'</span><span class="ContentPasted3">;</span></span></div>
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<span><span class="ContentPasted3">timelock_allexp = ft_timelockanalysis(cfg, eegData);</span></span></div>
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<span><span class="ContentPasted3">cfg = [];</span></span></div>
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<span><span class="ContentPasted3">cfg.covariance = </span><span style="color: rgb(167, 9, 245);" class="ContentPasted3">'yes'</span><span class="ContentPasted3">;</span></span></div>
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<span><span class="ContentPasted3">cfg.covariancewindow = </span><span style="color: rgb(167, 9, 245);" class="ContentPasted3">'all'</span><span class="ContentPasted3">;</span></span></div>
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<span><span class="ContentPasted3">cfg.keeptrials = </span><span style="color: rgb(167, 9, 245);" class="ContentPasted3">'yes'</span><span class="ContentPasted3">;</span></span></div>
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<span><span class="ContentPasted3">timelock_allexp_all = ft_timelockanalysis(cfg, eegData);</span></span></div>
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<span><span style="color: rgb(0, 128, 19);" class="ContentPasted3">%General source localisation</span></span></div>
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<span><span class="ContentPasted3">cfg = [];</span></span></div>
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<span><span class="ContentPasted3">cfg.headmodel = vol;</span></span></div>
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<span><span class="ContentPasted3">cfg.elec = timelock_allexp.elec;</span></span></div>
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<span><span class="ContentPasted3">cfg.grid = grid;</span></span></div>
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<span><span class="ContentPasted3">cfg.method = </span><span style="color: rgb(167, 9, 245);" class="ContentPasted3">'lcmv'</span><span class="ContentPasted3">;</span></span></div>
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<span><span class="ContentPasted3">cfg.lcmv.fixedori = </span><span style="color: rgb(167, 9, 245);" class="ContentPasted3">'yes'</span><span class="ContentPasted3">; </span><span style="color: rgb(0, 128, 19);" class="ContentPasted3">%Project onto largest
variance orientation</span></span></div>
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<span><span class="ContentPasted3">cfg.lcmv.keepfilter = </span><span style="color: rgb(167, 9, 245);" class="ContentPasted3">'yes'</span><span class="ContentPasted3">;
</span><span style="color: rgb(0, 128, 19);" class="ContentPasted3">%Keep the beamformer weights</span></span></div>
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<span><span class="ContentPasted3">cfg.lcmv.lambda = </span><span style="color: rgb(167, 9, 245);" class="ContentPasted3">'5%'</span><span class="ContentPasted3">;
</span><span style="color: rgb(0, 128, 19);" class="ContentPasted3">%Regularise a little</span></span></div>
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<span><span class="ContentPasted3">source_allexp = ft_sourceanalysis(cfg, timelock_allexp);</span></span></div>
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<span><span class="ContentPasted3">cfg = [];</span></span></div>
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<span><span class="ContentPasted3">cfg.method = </span><span style="color: rgb(167, 9, 245);" class="ContentPasted3">'nearest'</span><span class="ContentPasted3">;</span></span></div>
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<span><span class="ContentPasted3">cfg.parameter = </span><span style="color: rgb(167, 9, 245);" class="ContentPasted3">'tissue'</span><span class="ContentPasted3">;</span></span></div>
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<span><span class="ContentPasted3">grid2 = ft_sourceinterpolate(cfg,atlas,grid);</span></span></div>
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<span><span class="ContentPasted3">grid2.tissue = fix(grid2.tissue);</span></span></div>
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<span><span class="ContentPasted3">grid2.tissuelabel = atlas.tissuelabel;</span></span></div>
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<span><span class="ContentPasted3">cfg = [];</span></span></div>
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<span><span class="ContentPasted3">cfg.parcellation = </span><span style="color: rgb(167, 9, 245);" class="ContentPasted3">'tissue'</span><span class="ContentPasted3">;</span></span></div>
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<span><span class="ContentPasted3">cfg.method = </span><span style="color: rgb(167, 9, 245);" class="ContentPasted3">'svd'</span><span class="ContentPasted3">;</span></span></div>
<span class="lineNode" style="font-size:10pt;font-family:Menlo, Monaco, Consolas, "Courier New", monospace;font-weight:normal"><span><span class="ContentPasted3">roiData = ft_virtualchannel(cfg,timelock_allexp_all,source_allexp,grid2);</span></span></span>
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