[FieldTrip] Parcellate the reconstructed source time series

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

1. For "ft_sourceparcellate" our functional data must be in the same as our atlas. For that, we need to interpolate the functional data to the atlas. However, the problem is that 'ft_sourceinterpolate'  is interpolating only "pow" and "coh" not "mom" (source time course ). In the documentation also ( http://www.fieldtriptoolbox.org/tutorial/networkanalysis/#connectivity-analysis-and-parcellation ) they are interpolating 'Coh' only, thus parcellating only coherence.

Why not just follow the suggestion as per the network tutorial, and compute the connectivity metric at the uninterpolated dipole positions?
Alternatively, if you need the univariate time courses parcellated, you may want to try and interpolate your atlas onto the source model that you used for source reconstruction, and then use the interpolated atlas for parcellation. Or, as a third option, you may want to create a source model that is based on the equivalent dipole positions as in your atlas so that you don’t need to interpolate your reconstructed sources.

Good luck,
Jan-Mathijs

J.M.Schoffelen, MD PhD
Senior Researcher, VIDI-fellow - PI, language in interaction
Telephone: +31-24-3614793
Physical location: room 00.028
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands








On Sun, 24 Feb 2019 at 01:27, Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen at donders.ru.nl<mailto:jan.schoffelen at donders.ru.nl>> wrote:
Could you be a bit more specific in your question? Right now, based on the quality of your question, it seems as if you haven’t spent much time searching the documentation yourself. For instance, http://www.fieldtriptoolbox.org/tutorial/networkanalysis/ would already give you some directions how to ‘parcellate’ your source level data. Also, if you look for ‘ft_sourceparcellate’ you’ll probably be able to sort out how to do it.

Jan-Mathijs


On 22 Feb 2019, at 14:51, Neeraj kumar <neeraj750kumar at gmail.com<mailto:neeraj750kumar at gmail.com>> wrote:

Dear Schoffelen,

Thank you for your answer. But I'm still confused about how to get parcellated source time series in fieldtrip. I have  1sec time series for around 6000  grids.

Neeraj

On Fri, 22 Feb 2019 at 17:46, Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen at donders.ru.nl<mailto:jan.schoffelen at donders.ru.nl>> wrote:

I want to parcellate the reconstructed source time series (~ 1000ms).
I have moments in source.avg.mom for around 6000 grids.
Additionally, do I need to perform some normalization on time series before or after parcellation to perform network analysis?

Well, at least you should compute a metric between pairs of time series that can be subjected to a network analysis. Whether or not this needs ‘some normalization’ depends on what you exactly want to achieve.

Best wishes,
Jan-Mathijs





J.M.Schoffelen, MD PhD
Senior Researcher, VIDI-fellow - PI, language in interaction
Telephone: +31-24-3614793
Physical location: room 00.028
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands



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