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<div class="">On 25 Mar 2019, at 16:30, Duru Gun Ozkan <<a href="mailto:durugun.ozkan@uniroma1.it" class="">durugun.ozkan@uniroma1.it</a>> wrote:</div>
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<div class="">Dear Fieldtrippers,</div>
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<div class="">Following the network analysis tutorial (on resting state EEG data in my case), I have some questions.</div>
<div class="">I would like to obtain Graph theory metrics for each subject. I can obtain the clustering coefficient, degree and betweenness measurements. However, I am having some trouble getting other measures.</div>
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<div class="">1 - To use charpath method, I have first used the distance method which results in a distance matrix that consists values from 1 to 4 and also Inf (cfg.threshold = .1). when I use the charpath method however, the only value I get is 1 for every
single subject. </div>
<div class="">I suspect I am going wrong somewhere but the tutorial (or the forum) hasn’t helped me find what’s wrong. </div>
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<div class="">%% %%%%%%%%%% DISTANCE METHOD %%%%%%%%%% %%</div>
<div class="">cfg = [];</div>
<div class="">cfg.method = 'distance';</div>
<div class="">cfg.parameter = 'cohspctrm';</div>
<div class="">cfg.threshold = .1;</div>
<div class="">IF_network_full_distance = ft_networkanalysis(cfg,IF_source_conn_coh);</div>
<div class=""> </div>
<div class=""> </div>
<div class="">%% %%%%%%%%%% charpath METHOD %%%%%%%%%% %% have to use output from nw analysis distance method</div>
<div class="">cfg = [];</div>
<div class="">cfg.method = 'charpath';</div>
<div class="">cfg.parameter = 'distance';</div>
<div class="">cfg.threshold = .1;</div>
<div class="">network_full_charpath = ft_networkanalysis(cfg,IF_network_full_distance);</div>
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<div>Have you tried to run ft_networkanalysis without the cfg.threshold specified, when computing the ‘charpath’?</div>
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<div class="">2 - Another issue is with parcellation.</div>
<div class="">I have matched every template, atlas, sourcemodel to each other. However, since the atlas that I can use with my data does not contain a parcellation field, I don’t think this is possible. </div>
<div class="">Has there been any developments on this part of network analysis? Or is there a work around that I am not seeing?</div>
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<div>There might be a question behind your question, e.g. something does not seem to work for you. For me it’s not clear what this is.</div>
<div>In general, it is not obligatory that the data-field used for the parcellation is called ‘parcellation’. In your case it seems to be called ‘tissue’. This should work, if properly processed.</div>
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<div>Please feel free to contribute to the development of the network analysis functionality by writing documentation, best practices, code.</div>
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<div>Best wishes,</div>
<div>Jan-Mathijs</div>
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
J.M.Schoffelen, MD PhD<br class="">
Associate PI, VIDI-fellow - PI, language in interaction<br class="">
Telephone: +31-24-3614793</div>
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Physical location: room 00.028</div>
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Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands<br class="">
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<div class="">% %% %%% PARCELLATE %%% %%</div>
<div class="">atlas = ft_read_atlas('C\fieldtrip-20190220\fieldtrip-20190220\template\sourcemodel\standard_sourcemodel3d10mm.mat');</div>
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<div class="">% and call ft_sourceinterpolate:</div>
<div class="">cfg = [];</div>
<div class="">cfg.interpmethod = 'nearest';</div>
<div class="">cfg.parameter = 'tissue';</div>
<div class="">sourcemodel2 = ft_sourceinterpolate(cfg, atlas, grid);</div>
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<div class="">Error using ft_sourceparcellate (line 108)</div>
<div class="">the source positions are not consistent with the parcellation, please use FT_SOURCEINTERPOLATE</div>
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<div class="">Thanks in advance for your help,</div>
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<div class="">Best,</div>
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<div class="">Duru Ozkan</div>
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<div class="">My full code is below:</div>
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<div class="">addpath('C:\MATLAB\fieldtrip-20190220\fieldtrip-20190220');</div>
<div class="">ft_defaults</div>
<div class="">%%</div>
<div class="">clear all</div>
<div class="">close all</div>
<div class="">%% Load Variables </div>
<div class="">sub = 'S001'; % Sub Num</div>
<div class="">dir = strcat('C:\\tACS_EEG_JA_DATA\',sub);</div>
<div class="">cd(dir)</div>
<div class="">dataica = load(strcat('C:\Users\BrainStem\Google Drive\tACS_EEG_JA_DATA\',sub,'\',sub,'_clean.mat'));</div>
<div class="">dataica = dataica.cleanData;</div>
<div class=""> </div>
<div class="">% load standard_mri</div>
<div class="">load standard_mri.mat</div>
<div class="">mri = ft_volumereslice([], mri); </div>
<div class="">mri = ft_convert_units(mri,'mm');</div>
<div class=""> </div>
<div class="">load standard_BEM.mat;</div>
<div class="">vol = ft_convert_units(vol,'mm');</div>
<div class=""> </div>
<div class="">electrodes = load('C:\\tACS_EEG_JA_DATA\Conn\elecRULEZ.mat');</div>
<div class="">electrodes = ft_convert_units(electrodes.elec,'mm');</div>
<div class=""> </div>
<div class="">%% compute grid</div>
<div class="">cfg = [];</div>
<div class="">cfg.elec = electrodes;</div>
<div class="">cfg.headmodel = vol;</div>
<div class="">cfg.grid.resolution = 10;</div>
<div class="">cfg.grid.unit = 'mm';</div>
<div class="">cfg.inwardshift = -1.5;</div>
<div class="">grid = ft_prepare_sourcemodel(cfg);</div>
<div class=""> </div>
<div class="">%% compute sensor level Fourier spectra, to be used for cross-spectral density computation.</div>
<div class="">cfg = [];</div>
<div class="">cfg.method = 'mtmfft';</div>
<div class="">cfg.output = 'fourier';</div>
<div class="">cfg.keeptrials = 'yes';</div>
<div class="">cfg.tapsmofrq = 2;</div>
<div class="">cfg.foi = 18.5;</div>
<div class="">IF_freq = ft_freqanalysis(cfg, dataica);</div>
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<div class="">%% do the source reconstruction</div>
<div class="">cfg = [];</div>
<div class="">cfg.frequency = IF_freq.freq;</div>
<div class="">cfg.method = 'pcc';</div>
<div class="">cfg.elec = electrodes;</div>
<div class="">cfg.grid = grid;</div>
<div class="">cfg.headmodel = vol;</div>
<div class="">cfg.keeptrials = 'yes';</div>
<div class="">cfg.pcc.keepmom = 'yes';</div>
<div class="">cfg.keepnoise = 'yes';</div>
<div class="">cfg.pcc.lambda = '10%';</div>
<div class="">cfg.pcc.projectnoise = 'yes';</div>
<div class="">cfg.pcc.fixedori = 'yes';</div>
<div class="">cfg.pcc.keepcsd = 'yes';</div>
<div class="">IF_source = ft_sourceanalysis(cfg, IF_freq);</div>
<div class="">IF_source_nai = ft_sourcedescriptives([], IF_source); % to get the neural-activity-index</div>
<div class=""> </div>
<div class="">%% plot the neural activity index (power/noise)</div>
<div class="">cfg = [];</div>
<div class="">cfg.method = 'surface';</div>
<div class="">cfg.funparameter = 'nai';</div>
<div class="">cfg.maskparameter = cfg.funparameter;</div>
<div class="">% cfg.funcolorlim = [0.0 8];</div>
<div class="">% cfg.opacitylim = [3 8];</div>
<div class="">cfg.opacitymap = 'rampup'; </div>
<div class="">cfg.funcolormap = 'jet';</div>
<div class="">cfg.colorbar = 'yes';</div>
<div class="">ft_sourceplot(cfg, IF_source_nai);</div>
<div class="">view([-90 30]);</div>
<div class="">light;</div>
<div class=""> </div>
<div class="">%% compute connectivity</div>
<div class="">IF_source_sparse = ft_source2sparse(IF_source);</div>
<div class=""> </div>
<div class="">cfg=[];</div>
<div class="">cfg.method ='coh';</div>
<div class="">cfg.complex = 'absimag';</div>
<div class="">IF_source_conn_coh = ft_connectivityanalysis(cfg, IF_source_sparse);</div>
<div class=""> </div>
<div class="">figure;imagesc(IF_source_conn_coh.cohspctrm);</div>
<div class=""> </div>
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<div class="">%% %%%%%%%%%% DISTANCE METHOD %%%%%%%%%% %%</div>
<div class="">cfg = [];</div>
<div class="">cfg.method = 'distance';</div>
<div class="">cfg.parameter = 'cohspctrm';</div>
<div class="">cfg.threshold = .1;</div>
<div class="">IF_network_full_distance = ft_networkanalysis(cfg,IF_source_conn_coh);</div>
<div class=""> </div>
<div class=""> </div>
<div class="">%% %%%%%%%%%% charpath METHOD %%%%%%%%%% %% have to use output from nw analysis distance method</div>
<div class="">cfg = [];</div>
<div class="">cfg.method = 'charpath';</div>
<div class="">cfg.parameter = 'distance';</div>
<div class="">cfg.threshold = .1;</div>
<div class="">network_full_charpath = ft_networkanalysis(cfg,IF_network_full_distance);</div>
<div class=""> </div>
<div class="">save network_full_charpath network_full_charpath</div>
<div class=""> </div>
<div class="">Variable_pathLength = charpath(network_full_distance.distance);</div>
<div class=""> </div>
<div class="">% %% %%% PARCELLATE %%% %%</div>
<div class="">atlas = ft_read_atlas('C:\Users\BrainStem\Documents\MATLAB\fieldtrip-20190220\fieldtrip-20190220\template\atlas\aal\ROI_MNI_V4.nii');</div>
<div class="">load('C:\Users\BrainStem\Documents\MATLAB\fieldtrip-20190220\fieldtrip-20190220\template\sourcemodel\standard_sourcemodel3d10mm.mat');</div>
<div class="">% and call ft_sourceinterpolate:</div>
<div class="">cfg = [];</div>
<div class="">cfg.interpmethod = 'nearest';</div>
<div class="">cfg.parameter = 'tissue';</div>
<div class="">sourcemodel2 = ft_sourceinterpolate(cfg, atlas, grid);</div>
<div class="">% sourcemodel2 = ft_convert_units(sourcemodel2,'mm');</div>
<div class=""> </div>
<div class="">cfg = [];</div>
<div class="">cfg.parcellation = 'tissue';</div>
<div class="">cfg.parameter = 'tissue';</div>
<div class="">parc_conn = ft_sourceparcellate(cfg, IF_source_conn_coh, sourcemodel2);</div>
<div class=""> </div>
<div class="">figure;imagesc(parc_conn.cohspctrm);</div>
<div class=""> </div>
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<div dir="ltr" class=""><i style="font-size:12.8px" class="">Duru G</i><span style="font-family:Calibri,sans-serif;font-size:14.6667px;text-align:justify" class=""><i class="">ü</i></span><i style="font-size:12.8px" class="">n </i><span style="font-family:Calibri,sans-serif;font-size:14.6667px;text-align:justify" class=""><i class="">Ö</i></span><i style="font-size:12.8px" class="">zkan</i>
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<div style="font-size:12.8px;color:rgb(136,136,136)" class=""><font size="1" face="trebuchet ms, sans-serif" class=""><b class="">Ph.D. student in Cognitive Social and Affective Neuroscience.<br class="">
</b></font></div>
<div style="font-size:12.8px;color:rgb(136,136,136)" class=""><font size="1" face="trebuchet ms, sans-serif" class=""><b class="">Department of Psychology.<br class="">
University of Rome "La Sapienza".<br class="">
Via dei Marsi 78 - 00185 - Roma.</b></font></div>
<div style="font-size:12.8px;color:rgb(136,136,136)" class=""><font size="1" face="trebuchet ms, sans-serif" class=""><b class=""> </b></font><b style="font-family:"trebuchet ms",sans-serif;font-size:x-small" class="">e-mail: <a href="mailto:vanessa.era@uniroma1.it" style="color:rgb(17,85,204)" target="_blank" class="">durugun.ozkan@uniroma1.it</a></b></div>
<div class=""><font color="#1155cc" size="1" class=""><u class=""><a href="https://agliotilab.org/lab-staff/phd-students/2nd-year#anchor" target="_blank" class="">https://agliotilab.org/lab-staff/phd-students/2nd-year#anchor</a></u></font><br class="">
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