[FieldTrip] EEG connectivity analysis - error with ft_sourceparcellate in whole brain connectivity tutorial
Rebecca Kenny
beckenny at student.ubc.ca
Wed Sep 16 01:08:29 CEST 2020
Hello Michael,
Thank you for your quick response! It seems I am still getting errors.
Index exceeds the number of array elements (0).
Error in ft_sourceinterpolate>my_interpn (line 726)
ft_progress(sel(1)/num, 'interpolating %.1f%%\n', 100*sel(1)/num);
Error in ft_sourceinterpolate (line 631)
av( sel) = my_interpn(fv, ax(sel), ay(sel), az(sel),
cfg.interpmethod, cfg.feedback);
There should not be anything wrong with my data and I have followed the
tutorial to a T. I am not sure what I am missing. I appreciate the help.
Rebecca
On Tue, Sep 15, 2020 at 3:36 PM Michael Glassen - Biomedical Engineer <
MGlassen at kesslerfoundation.org> wrote:
> 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> 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> 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
>>
>> _______________________________________________
>> fieldtrip mailing list
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> https://doi.org/10.1371/journal.pcbi.1002202
>>
>>
>>
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