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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-US">Dear Community,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I am working on a MEG dataset and would like to calculate task-related whole-brain connectivity in one specific frequency band. As I am running into memory issues, I would like to calculate the imaginary coherence on
parcellated data (aal atlas). However, I am having trouble doing so, as after the parcellation the data structure/dimord is changed and ft_connectivityanalysis is not working anymore.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Does anyone have any suggestions? I was working along the tutorial “ Whole brain connectivity and network analysis” . Your help is much appreciated!
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Many thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Fanny<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Here is the code I am using (Fieldtrip 20220216, macOs, Matlab R2021b) :
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">%% interpolate template sourcemodel and atlas<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">load(fullfile(templatedir,
<span style="color:#AA04F9">'standard_sourcemodel3d8mm'</span>)); <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">atlas = ft_read_atlas(fullfile(templatedir,
<span style="color:#AA04F9">'ROI_MNI_V4.nii'</span>));<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">atlas = ft_convert_units(atlas,<span style="color:#AA04F9">'mm'</span>);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">sourcemodel = ft_convert_units(sourcemodel,<span style="color:#AA04F9">'mm'</span>);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.interpmethod =
<span style="color:#AA04F9">'nearest'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.parameter =
<span style="color:#AA04F9">'tissue'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">sourceatlas = ft_sourceinterpolate(cfg, atlas, sourcemodel);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">sourceatlas.pos=sourcemodel.pos;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">%% frequency analysis of sensor level timeseries data<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg=[];<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.method=<span style="color:#AA04F9">'mtmfft'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.output=<span style="color:#AA04F9">'fourier'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.keeptrials=<span style="color:#AA04F9">'yes'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.tapsmofrq=tapsmofreq;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.foi=foi;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.polyremoval=1;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">freq_all=ft_freqanalysis(cfg,data_all);
<span style="color:#028009">% for common filter</span><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">freq=ft_freqanalysis(cfg,data_act); % activation
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">freqBase=ft_freqanalysis(cfg,data_base);% baseline<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">%% PPC<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;color:#028009;mso-fareast-language:DE">% calculate common filter</span><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg=[];<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.frequency=freq.freq;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.method=<span style="color:#AA04F9">'pcc'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.sourcemodel=leadfield;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.elec = freq_all.grad;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.headmodel=headmodel;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.rawtrials =
<span style="color:#AA04F9">'yes'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.keeptrials =
<span style="color:#AA04F9">'yes'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.pcc.lambda=<span style="color:#AA04F9">'10%'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.pcc.projectnoise=<span style="color:#AA04F9">'yes'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.pcc.keepfilter=<span style="color:#AA04F9">'yes'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">source_all=ft_sourceanalysis(cfg,freq_all);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;color:#028009;mso-fareast-language:DE">% apply filter</span><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.sourcemodel.filter = source_all.avg.filter;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">source = ft_sourceanalysis(cfg, freq);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">sourceBase = ft_sourceanalysis(cfg, freqBase);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg=[];<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">source=ft_sourcedescriptives(cfg,source);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">sourceBase=ft_sourcedescriptives(cfg,sourceBase);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">% task related data<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.parameter =
<span style="color:#AA04F9">'avg.mom'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.operation =
<span style="color:#AA04F9">'((x1-x2)./x2)'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">sourceRel=ft_math(cfg,source,sourceBase);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">% parcellation<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">sourceRel.pos=sourcemodel.pos;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">sourceRel.dim=sourcemodel.dim;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg=[];<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.method=<span style="color:#AA04F9">'mean'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">cfg.parameter=<span style="color:#AA04F9">'mom'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">parc=ft_sourceparcellate(cfg,sourceRel,sourceatlas);
<span style="color:#028009">% also does not work with source_all</span><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">sourceRel =
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"> freq: 75.8735<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"> dim: [20 25 22]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"> pos: [11000×3 double]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"> label: {272×1 cell}<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"> mom: {11000×1 cell}<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"> inside: [11000×1 logical]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"> trialinfo: [235×10 double]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"> cfg: [1×1 struct]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">parc =
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"> freq: 75.8735<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"> cumtapcnt: [470×1 double]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"> label: {1×116 cell}<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"> mom: [116×3×5170 double]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"> momdimord: 'chan_ori_rpttap'<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"> brainordinate: [1×1 struct]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"> cfg: [1×1 struct]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">% Connectivity Analysis<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"> cfg=[];<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"> cfg.method=<span style="color:#AA04F9">'coh'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"> cfg.complex=<span style="color:#AA04F9">'absimag'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"> sourceConn=ft_connectivityanalysis(cfg,parc);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">Error using getdimord (line 42)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">field "crsspctrm" not present in data<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE">Error in ft_connectivityanalysis (line 634)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:Menlo;mso-fareast-language:DE"> data.dimord = ['rpt_' getdimord(data, inparam)];<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<br><div><hr style="color: #999999;" size="1"><p style="font-size: x-small; color: #999999;">Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | <a href="http://www.uke.de/">www.uke.de</a><br>Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel</p><hr style="color: #999999;" size="1"><p style="font-size: x-small; color: #999999;">SAVE PAPER - THINK BEFORE PRINTING</p></div></body>
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