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Hi Jan-Mathijs,</div>
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Thank you for the quick response! Both timelockstatistics and freqstatistics are exactly what im looking for! I played around with both functions, but I'm running into some issues preparing neighbors. Because I'm using the brainetome atlas on a volumetric headmodel,
I cant use ft_prepareneighbors if I understand correctly. So I was going to create my own neighbor template, by picking a threshold distance and for each roi in the atlas, calculating the distance from the center of each roi to all others and any pairs that
are below the threshold distance will be marked as neighbors. Would you have any suggestions on a distance to use, and does this approach seem sound? I tried running a quick analysis without neighbors(just clustering based on freq and time) on one subject
between 2 conditions. 2 negative clusters were found significant, each cluster consisting of only one roi(out of the whole 246 from the atlas). Im hoping by including neighbors into the analysis that it will be improved.</div>
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Thank you again for your help!</div>
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Best,</div>
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Michael Glassen</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> fieldtrip <fieldtrip-bounces@science.ru.nl> on behalf of Schoffelen, J.M. (Jan Mathijs) via fieldtrip <fieldtrip@science.ru.nl><br>
<b>Sent:</b> Tuesday, August 15, 2023 5:30 AM<br>
<b>To:</b> FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Cc:</b> Schoffelen, J.M. (Jan Mathijs) <janmathijs.schoffelen@donders.ru.nl><br>
<b>Subject:</b> Re: [FieldTrip] Running source statistics on atlas virtual channel</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space">Hi Michael,
<div class=""><br class="">
</div>
<div class="">If you want to run a statistical test on virtual channel data, you’d need to run ft_timelockstatistics, or ft_freqstatistics, depending on how you further processed the virtual channel data.</div>
<div class="">I would not recommend to use ft_virtualchannel to create a data object using all source dipole positions, because that leads to uncontrollable increase in RAM requirements.</div>
<div class="">I think that the particular error you get refers to an incorrect usage of ft_virtualchannel. I would think that it is correctly described in the help of the function, but in case you want to define virtual channels based on a set of dipole positions
that are defined within the original source data object, you don’t need to input a fourth atlas-like data structure.</div>
<div class=""><br class="">
</div>
<div class="">Good luck,</div>
<div class="">Jan-Mathijs</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 14 Aug 2023, at 17:36, Michael Glassen via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
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<div class="">
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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$" originalsrc="https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/example/source_statistics/__;!!HJOPV4FYYWzcc1jazlU!8NKHjd2nuO01v9keAIF1QkHk0sbso2-hl8vMMB6nGjuogzDUXWGBsf9c6DhnkJR5YuewKW4EtUMJR6ctlQ1XD391dPVp$" shash="RozS7xm2AJWflnqQXYVeBoCtXCt9grmSnFa91e7LTmq8ow2ENipOb1oypWhvnHTJO1/UElJIVQqvVHrN3kPdqrPBDeVZXp/kcVcdJFExrhnyuuxtO2wdHU1qT1RAElCH0F9sDotTTs02dg6PpPNVTqlHXcATr/eHxqW+cwBRZVY=" originalsrc="https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/example/source_statistics/__;!!HJOPV4FYYWzcc1jazlU!8NKHjd2nuO01v9keAIF1QkHk0sbso2-hl8vMMB6nGjuogzDUXWGBsf9c6DhnkJR5YuewKW4EtUMJR6ctlQ1XD391dPVp$" shash="nJIyd0ixmX98FMl0sg80fSRQSXzGB2ue5hEn3HZN3LCsJFXI4IoBU9Z3mVqVhRIYEO1nFAMPVny6+3AVH85Gp+x5USVrp+gQT2+z+BdlMd4UgUG8v04MEJ0MlrgbZnKL1MT+0Q2m46cuEh1HJH9cHoDpP4ox3JAtulZgK5PpCG4=" class="x_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="x_rtcContent" style="padding:30px"><span class="x_lineNode" style="font-size:10pt; font-family:Menlo,Monaco,Consolas,"Courier New",monospace; font-weight:normal"><span class=""><span class="x_ContentPasted2">cfg = [];</span></span></span>
<div class="x_lineNode" style="font-size:10pt; font-family:Menlo,Monaco,Consolas,"Courier New",monospace; font-weight:normal">
<span class=""><span class="x_ContentPasted2">cfg.pos = source_allexp.pos;</span></span></div>
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<span class=""><span class="x_ContentPasted2">cfg.method =<span class="x_Apple-converted-space"> </span></span><span class="x_ContentPasted2" style="color:rgb(167,9,245)">'svd'</span><span class="x_ContentPasted2">;</span></span></div>
<span class="x_lineNode" style="font-size:10pt; font-family:Menlo,Monaco,Consolas,"Courier New",monospace; font-weight:normal"><span class=""><span class="x_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="x_ContentPasted1">for dipole with position [-68 -104 -52].</div>
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<div class="x_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>
<div class="x_ContentPasted1"><br class="">
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<div class="x_ContentPasted1">I am using the template standard bem headmodel and the template brainnetom atlas <span class="x_ContentPasted5" style="font-family:Menlo,Monaco,Consolas,"Courier New",monospace; font-size:13.3333px; color:rgb(167,9,245); background-color:rgb(255,255,255); display:inline!important">BNA_MPM_thr25_1.25mm.nii</span>
<div class="x_rtcContent" style="padding:30px"><span class="x_lineNode" style="font-size:10pt; font-family:Menlo,Monaco,Consolas,"Courier New",monospace; font-weight:normal"><span class=""><span class="x_ContentPasted4" style="color:rgb(167,9,245)"></span></span></span></div>
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<div class="x_ContentPasted1">Best,</div>
<div class="x_ContentPasted1">Michael Glassen</div>
<div class="x_ContentPasted1"><br class="">
</div>
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<div class="x_ContentPasted1">%% Code</div>
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<span class=""><span class="x_ContentPasted3">cfg = [];</span></span></div>
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<span class=""><span class="x_ContentPasted3">cfg.method =<span class="x_Apple-converted-space"> </span></span><span class="x_ContentPasted3" style="color:rgb(167,9,245)">'project'</span><span class="x_ContentPasted3">;<span class="x_Apple-converted-space"> </span></span><span class="x_ContentPasted3" style="color:rgb(0,128,19)">%
onto scalp surface</span></span></div>
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<span class=""><span class="x_ContentPasted3">cfg.headshape = headmodel.bnd(scalp_index);<span class="x_Apple-converted-space"> </span></span><span class="x_ContentPasted3" style="color:rgb(0,128,19)">% scalp surface</span></span></div>
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<div class="x_lineNode" style="font-size:10pt; font-family:Menlo,Monaco,Consolas,"Courier New",monospace; font-weight:normal">
<span class=""><span class="x_ContentPasted3">eegData.elec = ft_electroderealign(cfg, eegData.elec);</span></span></div>
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<div class="x_lineNode" style="font-size:10pt; font-family:Menlo,Monaco,Consolas,"Courier New",monospace; font-weight:normal">
<span class=""><span class="x_ContentPasted3">cfg = [];</span></span></div>
<div class="x_lineNode" style="font-size:10pt; font-family:Menlo,Monaco,Consolas,"Courier New",monospace; font-weight:normal">
<span class=""><span class="x_ContentPasted3">cfg.headmodel = headmodel;</span></span></div>
<div class="x_lineNode" style="font-size:10pt; font-family:Menlo,Monaco,Consolas,"Courier New",monospace; font-weight:normal">
<span class=""><span class="x_ContentPasted3">cfg.elec = eegData.elec;</span></span></div>
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<span class=""><span class="x_ContentPasted3">cfg.grid.resolution = 4;</span></span></div>
<div class="x_lineNode" style="font-size:10pt; font-family:Menlo,Monaco,Consolas,"Courier New",monospace; font-weight:normal">
<span class=""><span class="x_ContentPasted3">cfg.grid.unit =<span class="x_Apple-converted-space"> </span></span><span class="x_ContentPasted3" style="color:rgb(167,9,245)">'mm'</span><span class="x_ContentPasted3">;</span></span></div>
<div class="x_lineNode" style="font-size:10pt; font-family:Menlo,Monaco,Consolas,"Courier New",monospace; font-weight:normal">
<span class=""><span class="x_ContentPasted3">cfg.channel =<span class="x_Apple-converted-space"> </span></span><span class="x_ContentPasted3" style="color:rgb(167,9,245)">'all'</span><span class="x_ContentPasted3">;</span></span></div>
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<span class=""><span class="x_ContentPasted3">grid = ft_prepare_leadfield(cfg);</span></span></div>
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<span class=""><span class="x_ContentPasted3">cfg = [];</span></span></div>
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<span class=""><span class="x_ContentPasted3">cfg.covariance =<span class="x_Apple-converted-space"> </span></span><span class="x_ContentPasted3" style="color:rgb(167,9,245)">'yes'</span><span class="x_ContentPasted3">;</span></span></div>
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<span class=""><span class="x_ContentPasted3">cfg.covariancewindow =<span class="x_Apple-converted-space"> </span></span><span class="x_ContentPasted3" style="color:rgb(167,9,245)">'all'</span><span class="x_ContentPasted3">;</span></span></div>
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<span class=""><span class="x_ContentPasted3">timelock_allexp = ft_timelockanalysis(cfg, eegData);</span></span></div>
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<span class=""><span class="x_ContentPasted3">cfg = [];</span></span></div>
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<span class=""><span class="x_ContentPasted3">cfg.covariance =<span class="x_Apple-converted-space"> </span></span><span class="x_ContentPasted3" style="color:rgb(167,9,245)">'yes'</span><span class="x_ContentPasted3">;</span></span></div>
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<span class=""><span class="x_ContentPasted3">cfg.covariancewindow =<span class="x_Apple-converted-space"> </span></span><span class="x_ContentPasted3" style="color:rgb(167,9,245)">'all'</span><span class="x_ContentPasted3">;</span></span></div>
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<span class=""><span class="x_ContentPasted3">cfg.keeptrials =<span class="x_Apple-converted-space"> </span></span><span class="x_ContentPasted3" style="color:rgb(167,9,245)">'yes'</span><span class="x_ContentPasted3">;</span></span></div>
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<span class=""><span class="x_ContentPasted3">timelock_allexp_all = ft_timelockanalysis(cfg, eegData);</span></span></div>
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<span class=""><span class="x_ContentPasted3" style="color:rgb(0,128,19)">%General source localisation</span></span></div>
<div class="x_lineNode" style="font-size:10pt; font-family:Menlo,Monaco,Consolas,"Courier New",monospace; font-weight:normal">
<span class=""><span class="x_ContentPasted3">cfg = [];</span></span></div>
<div class="x_lineNode" style="font-size:10pt; font-family:Menlo,Monaco,Consolas,"Courier New",monospace; font-weight:normal">
<span class=""><span class="x_ContentPasted3">cfg.headmodel = vol;</span></span></div>
<div class="x_lineNode" style="font-size:10pt; font-family:Menlo,Monaco,Consolas,"Courier New",monospace; font-weight:normal">
<span class=""><span class="x_ContentPasted3">cfg.elec = timelock_allexp.elec;</span></span></div>
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<span class=""><span class="x_ContentPasted3">cfg.grid = grid;</span></span></div>
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<span class=""><span class="x_ContentPasted3">cfg.method =<span class="x_Apple-converted-space"> </span></span><span class="x_ContentPasted3" style="color:rgb(167,9,245)">'lcmv'</span><span class="x_ContentPasted3">;</span></span></div>
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<span class=""><span class="x_ContentPasted3">cfg.lcmv.fixedori =<span class="x_Apple-converted-space"> </span></span><span class="x_ContentPasted3" style="color:rgb(167,9,245)">'yes'</span><span class="x_ContentPasted3">; </span><span class="x_ContentPasted3" style="color:rgb(0,128,19)">%Project
onto largest variance orientation</span></span></div>
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<span class=""><span class="x_ContentPasted3">cfg.lcmv.keepfilter =<span class="x_Apple-converted-space"> </span></span><span class="x_ContentPasted3" style="color:rgb(167,9,245)">'yes'</span><span class="x_ContentPasted3">;<span class="x_Apple-converted-space"> </span></span><span class="x_ContentPasted3" style="color:rgb(0,128,19)">%Keep
the beamformer weights</span></span></div>
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<span class=""><span class="x_ContentPasted3">cfg.lcmv.lambda =<span class="x_Apple-converted-space"> </span></span><span class="x_ContentPasted3" style="color:rgb(167,9,245)">'5%'</span><span class="x_ContentPasted3">;<span class="x_Apple-converted-space"> </span></span><span class="x_ContentPasted3" style="color:rgb(0,128,19)">%Regularise
a little</span></span></div>
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<span class=""><span class="x_ContentPasted3">source_allexp = ft_sourceanalysis(cfg, timelock_allexp);</span></span></div>
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<span class=""><span class="x_ContentPasted3">cfg = [];</span></span></div>
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<span class=""><span class="x_ContentPasted3">cfg.method =<span class="x_Apple-converted-space"> </span></span><span class="x_ContentPasted3" style="color:rgb(167,9,245)">'nearest'</span><span class="x_ContentPasted3">;</span></span></div>
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<span class=""><span class="x_ContentPasted3">cfg.parameter =<span class="x_Apple-converted-space"> </span></span><span class="x_ContentPasted3" style="color:rgb(167,9,245)">'tissue'</span><span class="x_ContentPasted3">;</span></span></div>
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<span class=""><span class="x_ContentPasted3">grid2 = ft_sourceinterpolate(cfg,atlas,grid);</span></span></div>
<div class="x_lineNode" style="font-size:10pt; font-family:Menlo,Monaco,Consolas,"Courier New",monospace; font-weight:normal">
<span class=""><span class="x_ContentPasted3">grid2.tissue = fix(grid2.tissue);</span></span></div>
<div class="x_lineNode" style="font-size:10pt; font-family:Menlo,Monaco,Consolas,"Courier New",monospace; font-weight:normal">
<span class=""><span class="x_ContentPasted3">grid2.tissuelabel = atlas.tissuelabel;</span></span></div>
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<span class=""><span class="x_ContentPasted3"><br class="">
</span></span></div>
<div class="x_lineNode" style="font-size:10pt; font-family:Menlo,Monaco,Consolas,"Courier New",monospace; font-weight:normal">
<span class=""><span class="x_ContentPasted3">cfg = [];</span></span></div>
<div class="x_lineNode" style="font-size:10pt; font-family:Menlo,Monaco,Consolas,"Courier New",monospace; font-weight:normal">
<span class=""><span class="x_ContentPasted3">cfg.parcellation =<span class="x_Apple-converted-space"> </span></span><span class="x_ContentPasted3" style="color:rgb(167,9,245)">'tissue'</span><span class="x_ContentPasted3">;</span></span></div>
<div class="x_lineNode" style="font-size:10pt; font-family:Menlo,Monaco,Consolas,"Courier New",monospace; font-weight:normal">
<span class=""><span class="x_ContentPasted3">cfg.method =<span class="x_Apple-converted-space"> </span></span><span class="x_ContentPasted3" style="color:rgb(167,9,245)">'svd'</span><span class="x_ContentPasted3">;</span></span></div>
<span class="x_lineNode" style="font-size:10pt; font-family:Menlo,Monaco,Consolas,"Courier New",monospace; font-weight:normal"><span class=""><span class="x_ContentPasted3">roiData = ft_virtualchannel(cfg,timelock_allexp_all,source_allexp,grid2);</span></span></span>
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<div class="x_ContentPasted1"><br class="">
</div>
<br class="">
</div>
<span class="" style="font-family:Helvetica; font-size:14px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">_______________________________________________</span><br class="" style="font-family:Helvetica; font-size:14px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span class="" style="font-family:Helvetica; font-size:14px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">fieldtrip
mailing list</span><br class="" style="font-family:Helvetica; font-size:14px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" originalsrc="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" shash="AUEKFwrp1EiRz3caFtNQx9wRfgfNBqyzEvx6X8H70AVXO4ffAELy9kx+rppPC9yQS/Tpq7N9spQXu/6PjJTETAiXnC6esKNVTRIXFRiAxIixDUnKL16Wi3A6Z4O2n93o9e9Lhb5DElpG4U7osrN6AQt+N94p3l6CbvtcutlrBNQ=" class="" style="font-family:Helvetica; font-size:14px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br class="" style="font-family:Helvetica; font-size:14px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<a href="https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!_rUj7Lyl6a_A9uIGgthQ4jhKPl_kBY3iYrzkr30L9qNkHtZ28mjD0GPJmS_V0CkzgfXaaUd_d3CWlPsfOPu9YdF8ZwGwPB3W9389Qg$" originalsrc="https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!_rUj7Lyl6a_A9uIGgthQ4jhKPl_kBY3iYrzkr30L9qNkHtZ28mjD0GPJmS_V0CkzgfXaaUd_d3CWlPsfOPu9YdF8ZwGwPB3W9389Qg$" shash="Gp8+mOe4SHs+3TS5QMhRcPj4gaN7OE4PFyeno0BhkXfoJjOVfh8Ep4PQ1js8+39FENwcekjlhmY+Ff/4XKmgk6TwAwqRdsr5lcwwDXg7J0DdfpUrk5yuLIDk4w0A+8x9zYpGkRjtpiiz7tr/VGkOrak+9VtmwsqJeGFU7cZplQ4=" class="" style="font-family:Helvetica; font-size:14px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">https://doi.org/10.1371/journal.pcbi.1002202</a></div>
</blockquote>
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