[FieldTrip] EEG connectivity analysis - error with ft_sourceparcellate in whole brain connectivity tutorial
Rebecca Kenny
beckenny at student.ubc.ca
Wed Sep 16 19:54:55 CEST 2020
Hello Jan-Mathijs,
Thank you for your help. I appreciate you taking the time to explain these
steps to me. I am slowly learning so thank you for your help. I will look
through the code and figure out where I am making a mistake.
Thank you again!
Rebecca
On Wed, Sep 16, 2020 at 12:22 AM Schoffelen, J.M. (Jan Mathijs) <
jan.schoffelen at donders.ru.nl> wrote:
> Hi Rebecca,
>
> Just some pointers below. One cannot ‘just’ interpolate one object to
> another one without considering (and validating) whether,
>
> 1) the coordinate system in which the objects are expressed are the same
> 2) the objects’ coordinates are expressed in the same metric units
> (although FT usually tries to check this, and fix it, if possible)
> 3) both objects are of a similar ’nature’, i.e. both defined as a 3D
> volume, or as a point cloud, or as a mesh. (although FT can toggle back and
> forth, it’s often not desirable)
> 4) the atlas you aim to use is appropriate for your data (particularly in
> light of point 3).
>
> Furthermore, the error you paste is pretty low level and not informative
> without any additional context. The only thing that I can derive from it,
> is that the variable ’ sel’ is most likely empty (i.e. contains 0 elements,
> which causes the error. What ’sel’ means in this context, and why it is
> empty in your case is can not be derived. Additional detective work is best
> done with you, by using the matlab debugger, which allows you to step
> through the code line-by-line to investigate the variables in the
> function’s workspace.
>
> Good luck,
>
> Jan-Mathijs
>
>
>
>
>
> On 16 Sep 2020, at 01:08, Rebecca Kenny <beckenny at student.ubc.ca> wrote:
>
> 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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