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Hi Rebecca,
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<div class="">The atlas needs to be represented as a proper atlas, also known as a ‘parcellation’. Unless you know what you’re doing, this can only be achieved if the specified atlas is either in a well defined mat-file, or if the atlas is created (i.e. read
from file + some additional wizardry applied to those data) by ft_read_atlas. I suspect that you did not do atlas = ft_read_atlas(‘AllAreas_v17_MPM.mat’); in order to create the atlas variable.</div>
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<div class="">Also, note that ft_sourceparcellate will try and make the parcellation according to the information in the named <cfg.parcellation> field. After calling ft_read_atlas for the AllAreas_v17_MPM file, this parcellation is defined in the (confusingly)
’tissue’ field, so cfg.parcellation should be ’tissue’.</div>
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<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
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<div class="">On 14 Sep 2020, at 20:41, Rebecca Kenny <<a href="mailto:beckenny@student.ubc.ca" class="">beckenny@student.ubc.ca</a>> wrote:</div>
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<div dir="ltr" class="">Hello,<br class="">
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I am attempting to run connectivity analysis on resting-state EEG data. <b class="">
My goal of source space analysis is to run <i class="">ft_networkanalysis</i> and extract graph theory variables. </b>I am following the "whole-brain connectivity and network analysis" tutorial. I believe I have successfully navigated the tutorial (after importing
my cleaned data from EEGlab) until I experience errors when I get to the 'connectivity analysis and parcellation'.<br class="">
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I can't find the atlas_MMP1.0_4k.mat file so I tried to use AllAreas_v17.mat.<br class="">
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<div class=""> % compute connectivity</div>
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<div class=""> cfg = [];</div>
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<div class=""> cfg.method ='coh';</div>
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<div class=""> cfg.complex = 'absimag';</div>
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<div class=""> source_conn = ft_connectivityanalysis(cfg, source);</div>
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<div class=""> load AllAreas_v17.mat;</div>
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<div class=""> atlas.pos = source_conn.pos; </div>
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<div class=""> cfg = [];</div>
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<div class=""> cfg.parcellation = 'parcellation';</div>
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<div class=""> cfg.parameter = 'cohspctrm';</div>
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<div class=""> parc_conn = ft_sourceparcellate(cfg, source_conn, atlas);</div>
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<div class=""> figure;imagesc(parc_conn.cohspctrm);</div>
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<div class="">Error using ft_checkdata (line 528)</div>
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<div class="">This function requires parcellation data as input, see ft_datatype_parcellation.</div>
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<div class="">Error in ft_sourceparcellate (line 97)</div>
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<div class="">parcellation = ft_checkdata(parcellation, 'datatype', 'parcellation', 'parcellationstyle', 'indexed');</div>
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<div class="">If there is an email thread already, please direct me to the proper post. </div>
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<div class="">I appreciate any help. I have been stuck at this part for a while and would love to move through my analysis.</div>
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<div class="">Thank you,</div>
<div class="">Rebecca </div>
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