[FieldTrip] problem using ft_sourceparcellate

[Johannes Gehrig]

Dear Stefan,

thanks for your reply. At the moment I use simple "coherence" following the „whole brain connectivity“ tutorial. However, if there was a memory efficient solution for dwPLI that is also an option. If I followed the discussion correctly, this is not yet fully implemented?

Have you tried to parcellate your data before doing the connectivity analysis? I suspect that my problem could be related with ft_sourceinterpollate, because the output of the source analysis (avg.csd, avg.mom, avg.noisecsd, computed withels pcc) is no longer present after ft_sourceinterpolate and without the source interpolation the source parcellation doesn't work, so far my impression...

Thanks and best regards,
Johannes

Von: Stefan Dvoretskii
Gesendet: Mittwoch, 6. Oktober 2021 17:39
An: FieldTrip discussion list
Cc: Johannes Gehrig; Gil Avila, Cristina
Betreff: Re: [FieldTrip] problem using ft_sourceparcellate

Dear Johannes, 

which connectivity measure are you using? There is a potential bottleneck in the 'ft_connectivityanalysis', which can however be circumvented with custom code, at least for dwPLI. Then you won't even need to parcelate.
We are currently working to incorporate it into the Fieldtrip code.

Best regards,
Stefan

пн, 4 окт. 2021 г., 11:06 Johannes Gehrig via fieldtrip <fieldtrip at science.ru.nl>:
Dear Fieldtrip-user,
I am facing a problem using ft_sourceinterpolate. I am following the "Whole brain connectivity and network analysis"- Tutorial and as I can not compute the connectivity directly with the source data ("out of memory") I would like to perform the source parcellation before computing the connectivity. Unfortunately (fieldtrip 20211001 and matlab2018b) ft_sourceparcellate crashes after calling it. Before computing the source data the sourcemodel was interpolated with the atlas using ft_sourceinterpolate. Therefore the amount of positions in the atlas and the source data is the same (8004).
load('atlas_MMP1.0_4k.mat'); 
cfg = [];
cfg.parcellation = 'parcellation';
cfg.method       = 'mean';
cfg.parameter    = 'all'; 
parc_sourceOn = ft_sourceparcellate(cfg, source_ON, atlas);
Error message:"
there are in total 8004 positions, 4544 positions are inside the brain, 8004 positions have a label
4544 of the positions inside the brain have a label
4544 of the labeled positions are inside the brain
0 of the positions inside the brain do not have a label
creating 362 parcels for parameter csd by taking the mean
computing parcellation
232           tmp(j,:,:) = cellmean1(dat(tissue==j));
computing parcellation for L_V1_ROI
Index exceeds array bounds.

Error in ft_sourceparcellate>cellmean1 (line 494)
y = x{1};

Error in ft_sourceparcellate (line 232)
          tmp(j,:,:) = cellmean1(dat(tissue==j));
"
Any help and ideas are very much appreciated!
Best regards, Johannes
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