[FieldTrip] Parcellate the reconstructed source time series

Tzvetan Popov tzvetan.popov at uni-konstanz.de
Tue Feb 26 09:43:48 CET 2019


Dear Neeraj,

in addition to Jan-Mathijs’ suggestions you should consider the following:

Compute the head model suited for EEG analysis. Type ‘EEG head model’ in the search field and browse thru the links that will pop up. Once you have your head model you could compute source model in accordance with some brain atlas. 
An example is provided here: http://www.fieldtriptoolbox.org/tutorial/salzburg/ <http://www.fieldtriptoolbox.org/tutorial/salzburg/>
In particular, the section http://www.fieldtriptoolbox.org/tutorial/salzburg/#localizing-auditory-evoked-fields-using-beamforming-techniques-in-parceled-brain-space <http://www.fieldtriptoolbox.org/tutorial/salzburg/#localizing-auditory-evoked-fields-using-beamforming-techniques-in-parceled-brain-space>
gives you an idea how to approach this. 
> 
> My final goal is to perform 'ft_connectivityanalysis(cfg, data)', where 'data' contains time series of all parcellated roi. It would be very helpful if you can help me with that.

Example of your final goal is illustrated here: http://www.fieldtriptoolbox.org/tutorial/salzburg/#connectivity-analysis <http://www.fieldtriptoolbox.org/tutorial/salzburg/#connectivity-analysis> using only 3 brain parcels. Yet, once you understand the pipeline you can easily extend to your preferred number of parcels. 

Good luck
Tzvetan

> 
> Thank you
> Neeraj
> 
> 
> 
> 
> 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/ <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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