[FieldTrip] Running the ICA method to remove EOG/ECG artifact on Neuromag(*.fif) data

[jan-mathijs schoffelen]

Hi Alex,

> I am curious to know if fieldtrip handles this properly? and if so how.

It depends a bit on the exact algorithm that is used, but for example the runica implementation (we use the EEGlab code for this) performs a whitening of the data prior to the decomposition. This would address the difference in magnitude issue, wouldn't it?

> Also can Fieldtrip write data back into fif files keeping intact
> all the measurement info?

Not really; I have some code of Lauri's (which is not yet in FT), which can write epoched data to a fif-file. However, most of the measurement info is lost along the way. Also, since we're not fif-experts, it's not trivial for us to find out how the measurement info should be formatted. Of course it is possible to reverse engineer this from the mne-code, but this is heavily geared towards elekta hardware. Yet, I could imagine that this functionality could be valuable, because it would enable two-way traffic of data between FT and MNE-suite. Do you happen to have any code that writes meaningful measurement info?

Best,

Jan-Mathijs


> 
> thanks
> 
> Alex
> -- 
> Alexandre Gramfort, PhD
> alexandre.gramfort at inria.fr
> INRIA Parietal Project Team, NeuroSpin CEA Saclay
> Bat. 145, PC 156
> 91191 Gif-sur-Yvette, France
> http://alexandre.gramfort.net
> 
> On Thu, Apr 12, 2012 at 7:21 PM, Candida Jane Maria Ustine
> <candida at nmr.mgh.harvard.edu> wrote:
>> Hello All,
>> 
>> I have just started reading about fieldtrip and I am learning a lot of
>> exciting things.
>> 
>> I have MEG data using the neuromag system and I wanted to run the
>> Independent Component Analysis on the .fif files to remove the EOG and ECG
>> artifact from them. I see that the documentation provided in the
>> website(http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts)
>> has resources to handle CTF datasets, and I was wondering if anyone has
>> looked into the option of using the .fif files directly.
>> Or is there a way to convert the *.fif files to the CTF format as there is
>> an MNE utility to do the reverse mne_ctf2fif?
>> 
>> Thanks much for your time and help!
>> 
>> Best,
>> Candida
>> 
>> 
>> 
>> --
>> Candida Jane Maria Ustine
>> Martinos Center for Biomedical Imaging
>> MGH
>> Kuperberg Lab
>> 
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Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

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