Saving preprocessed data in a raw MEG format

Laurence Hunt lhunt at FMRIB.OX.AC.UK
Tue Jul 13 14:17:46 CEST 2010


Hi Geoff - 

I've used both MNE and fieldtrip, but I think writing .fif files can be problematic - there isn't an easy way to do it as it requires a lot of headers etc. to be written, and (as far as I know) there's no matlab toolbox to do this at the moment (the best fiff matlab toolbox (primarily for reading, rather than writing, files) is the one bundled with MNE). 

The thing that might be best would be to compute a file that *looks like* the appropriate .fif file - e.g. a simple ERP, using mne_process_raw - and then *overwrite* the ERP with the stuff you have generated in matlab. The best people to advise you with this part might not be fieldtrip users, but the MNE community (e.g. Matti Hamalainen), mostly based at MGH. 

But there might be CTF users who could give you advice on writing .ds files - I use a Neuromag scanner myself so don't know anything about the CTF file format.

Hope this helps.

Laurence

===========================================
Laurence Hunt, DPhil Student
 Centre for Functional MRI of the Brain (FMRIB), 
University of Oxford
lhunt at fmrib.ox.ac.uk
Phone: (+44)1865-(2)22738
===========================================

On 13 Jul 2010, at 11:33, Geoff Brookshire wrote:

> Hello,
> 
> I'm working on source localization of MEG ERPs, and have run into a couple issues that I'm hoping someone will have some experience with. I'm using MNE software to perform the localization, since Fieldtrip is only able to do this on time-frequency data now.  The thing is that I've already done pretty extensive preprocessing in Fieldtrip and so can't afford to ditch that.  My hope is that I'll be able to output this preprocessed data from Fieldtrip in a format that MNE can read.
> 
> I've seen people talking here recently about a similar issue, but that thread ("Export EEG Data") seemed to deal very specifically with the brainvision_eeg format.
> 
> I've been hoping to export the data as a .ds directory, as it was originally saved.  MNE can convert CTF .ds directories to .fif (the format it normally uses), but I don't think this is a possible output format for ft_write_data.
> 
> Any ideas anyone has on how to proceed would be greatly appreciated!
> 
> Thanks,
> Geoff Brookshire
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
> 

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.



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