[FieldTrip] EEG connectivity analysis - error with ft_sourceparcellate in whole brain connectivity tutorial

[Schoffelen, J.M. (Jan Mathijs)]

Hi Rebecca,

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.

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’.

Best wishes,
Jan-Mathijs



On 14 Sep 2020, at 20:41, Rebecca Kenny <beckenny at student.ubc.ca<mailto:beckenny at student.ubc.ca>> wrote:

Hello,

I am attempting to run connectivity analysis on resting-state EEG data.  My goal of source space analysis is to run ft_networkanalysis and extract graph theory variables. 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'.

I can't find the atlas_MMP1.0_4k.mat file so I tried to use AllAreas_v17.mat.

  % compute connectivity
    cfg         = [];
    cfg.method  ='coh';
    cfg.complex = 'absimag';
    source_conn = ft_connectivityanalysis(cfg, source);

    load AllAreas_v17.mat;
    atlas.pos = source_conn.pos;

    cfg = [];
    cfg.parcellation = 'parcellation';
    cfg.parameter    = 'cohspctrm';
    parc_conn = ft_sourceparcellate(cfg, source_conn, atlas);

    figure;imagesc(parc_conn.cohspctrm);


Error using ft_checkdata (line 528)
This function requires parcellation data as input, see ft_datatype_parcellation.

Error in ft_sourceparcellate (line 97)
parcellation = ft_checkdata(parcellation, 'datatype', 'parcellation', 'parcellationstyle', 'indexed');

If there is an email thread already, please direct me to the proper post.

I appreciate any help.  I have been stuck at this part for a while and would love to move through my analysis.

Thank you,
Rebecca

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