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

[Michael Glassen - Biomedical Engineer]

Hi Rebecca,

I have run into similar issues, I may be wrong but I believe interpolating the atlas onto your source model will solve this issue. I grabbed some code from one of the tutorials and pasted below, try it out and see if it fixes your error, replacing the atlas and sourcemodel variables with whatever you’ve named them in your script.

Best,
Michael Glassen

%%
cfg = [];
cfg.interpmethod = 'nearest';
cfg.parameter = 'tissue';
newAtlas = ft_sourceinterpolate(cfg, atlas, sourcemodel);

________________________________
From: fieldtrip <fieldtrip-bounces at science.ru.nl> on behalf of Rebecca Kenny <beckenny at student.ubc.ca>
Sent: Tuesday, September 15, 2020 5:54:12 PM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] EEG connectivity analysis - error with ft_sourceparcellate in whole brain connectivity tutorial

Hello Jan-Mathijs,

Thank you very much for your reply! It seems to have worked and I am really appreciative.  I now have a new error that maybe you can help with.  Would this be because of the atlas I chose?

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

there are in total 4050 positions, 2015 positions are inside the brain, 701027 positions have a label
0 of the positions inside the brain have a label
The logical indices contain a true value outside of the array bounds.

Error in ft_sourceparcellate (line 172)
  fprintf('%d of the labeled positions are inside the brain\n',         sum(source.inside(seg(:)~=0)));

Thank you,
Rebecca


On Mon, Sep 14, 2020 at 10:50 PM Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen at donders.ru.nl<mailto:jan.schoffelen at donders.ru.nl>> wrote:
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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