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Hi Christian,
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<div class="">I guess you need to figure out why the dimension of the coherence matrix does not match the expectations.</div>
<div class="">Based on the information you provide (i.e. the lack thereof: it’s not clear how you compute SourceData, and how you spectrally transformed your sensor data that goes into the source reconstruction step) there is lottle to go on.</div>
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<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
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<div class="">On 21 May 2019, at 19:27, Christian Mista <<a href="mailto:cmista@ingenieria.uner.edu.ar" class="">cmista@ingenieria.uner.edu.ar</a>> wrote:</div>
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Hi FieldTrip community,</div>
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I've been trying to perform a connectivity analysis using a 66 eeg recording database. So far, I've being able to solve the sourceanalysis (following the tutorial
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http://www.fieldtriptoolbox.org/tutorial/networkanalysis/</a>) and plot the source activity. However, the problem starts when I'm trying the connectivity analysis. Any grid dimension lower than 20 mm in the sourcemodel calculation results in a matlab error
(Out of memory) in the connectivity analysis. I guess that a grid dimension lower than 20 mm conveys to huge matrix sizes, not manageable by my OS (linux + Matlab).
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%% This is how I compute the sourcemodel (run ok)<br class="">
cfg = [];<br class="">
cfg.elec = data.elec;<br class="">
cfg.elec.unit = 'mm'; % unit in cm<br class="">
cfg.headmodel = headmodel;<br class="">
cfg.grid.resolution = 20; % use a 3-D grid with a 20 mm resolution<br class="">
[lf] = ft_prepare_leadfield(cfg);</div>
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After computing the sourcemodel using the 20 mm grid, I have issues to parcellate my data. My main concern is about the mismatch size between the connectivity matrix and the atlas.
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source_conn =<br class="">
dim: [7 9 8]<br class="">
inside: [504×1 logical]<br class="">
pos: [504×3 double]<br class="">
cohspctrm: [5544×5544 double]<br class="">
dimord: 'pos_pos_freq'<br class="">
freq: 10<br class="">
cfg: [1×1 struct]</div>
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atlas = <br class="">
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dim: [91 109 91]<br class="">
hdr: [1×1 struct]<br class="">
transform: [4×4 double]<br class="">
unit: 'mm'<br class="">
tissue: [91×109×91 double]<br class="">
tissuelabel: {1×116 cell}<br class="">
coordsys: 'mni'</div>
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I'd tried to interpolate and parcellate the matrix, but I must be missing or confusing something... Below is the code to calculate the connectivity and the parcellation.
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%% connectivity<br class="">
cfg = [];<br class="">
cfg.method = 'coh';<br class="">
cfg.complex = 'absimag';<br class="">
source_conn = ft_connectivityanalysis(cfg, SourceData);<br class="">
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%The conectome<br class="">
figure;imagesc(source_conn.cohspctrm); %5544x5544 double<br class="">
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%Parcellation<br class="">
atlas = ft_read_atlas('/fieldtrip-master/template/atlas/aal/ROI_MNI_V4.nii');<br class="">
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cfg = [];<br class="">
cfg.interpmethod='nearest';<br class="">
cfg.parameter='tissue';<br class="">
[int_atlas] = ft_sourceinterpolate(cfg, atlas, source_conn);<br class="">
int_atlas.pos = source_conn.pos; % otherwise the parcellation won't work<br class="">
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% and call ft_sourceparcellate:<br class="">
cfg = [];<br class="">
cfg.parcellation = 'tissue';<br class="">
cfg.parameter = 'cohspctrm';<br class="">
parc_conn = ft_sourceparcellate(cfg, source_conn, int_atlas);<br class="">
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figure;imagesc(parc_conn.cohspctrm);<br class="">
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++Error in command windows matlab <br class="">
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there are in total 504 positions, 230 positions are inside the brain, 181 positions have a label<br class="">
168 of the positions inside the brain have a label<br class="">
168 of the labeled positions are inside the brain<br class="">
62 of the positions inside the brain do not have a label<span style="color:rgb(255,0,0)" class=""><span style="background-color:rgb(255,0,0)" class=""><br class="">
<span style="background-color:rgb(255,255,255)" class="">Error using ft_notification (line 340)<br class="">
unsupported dimord unknown_unknown_freq<br class="">
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Error in ft_error (line 39)<br class="">
ft_notification(varargin{:});<br class="">
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Error in ft_sourceparcellate (line 309)<br class="">
ft_error('unsupported dimord %s', dimord{i})</span></span></span></div>
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Two questions <br class="">
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-Is 20 mm the min grid size to calculate connectivity?</div>
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-What I'm missing in the parcellation process?</div>
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I would really appreciate any advice, I've been scratching my head for a while on this one.</div>
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Best,</div>
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Christian </div>
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