CTF 3rd order gradiometers correction

Vladimir Litvak v.litvak at ION.UCL.AC.UK
Thu Jul 10 14:34:19 CEST 2008


Dear Michael,

You don't need to wait. You just need to be careful. The version
presently available on the FTP server supports reading CTF datasets
with denoising. Just see my remarks from the e-mails before. You
should specify:

cfg.headerformat = 'ctf_new';
cfg.dataformat = 'ctf_new';

for preprocessing and also specify ctf_new in read_data and
read_header if you call them directly.

The signs that you are using the right reader (from external ctf
toolbox) are that there is a disclaimer message appearing every time
you read something and if you do imagesc(log(abs(grad.tra))) for a 3rd
gradient dataset, you'll see that there is a lot happening on the
right side of the matrix related to reference sensors (for the wrong
reader you'll just see some straight lines).

Then use the data and the grad normally. To be careful I'd suggest you
to test your results thoroughly. Try to do the same analysis with
'raw' and 3rd gradient. Also you can try converting with either CTF
software or denoise_synthetic and compare the results (for
denoise_synthetic to work you must use the new reader).

The more people do this kind of tests and report their results, the
more confident we'll become of the new code and the sooner Robert will
make it default.

Good luck,

Vladimir


On Thu, Jul 10, 2008 at 1:05 PM, Michael Wibral
<wibral at bic.uni-frankfurt.de> wrote:
> Dear Vladimir,
>
> I understand the problem about leadfields for 3rd gradients and magnetometers to be different. I am just curious now how to best proceed, when the measured data are from a rather noisy inner city environment:
> (1) Go for the raw data and increase the artefact rejection thresholds considerably (as beamforming should not localize artefacts inside the head anyway).
> (2) Wait for a fieldtrip version where leadfield can be computed for 3rd grads (if that's planned at all...).
> (3) try to use laedfields from CTF for these data, if that's possible.
>
> Thanks for any suggestions on this issue.
>
> Best,
> Michael
>
>
>> -----Urspr√ľngliche Nachricht-----
>> Von: "Vladimir Litvak" <v.litvak at ION.UCL.AC.UK>
>> Gesendet: 09.07.08 19:34:51
>> An: FIELDTRIP at NIC.SURFNET.NL
>> Betreff: Re: [FIELDTRIP] CTF 3rd order gradiometers correction
>
>
>> Until the recent improvements (which are not yet default) fieldtrip
>> assumed that the data is 'raw'. Therefore source reconstruction was
>> not precise for data that was saved in 3rd gradient. The data is
>> indeed read as it's saved so for sensor level analysis there is no
>> problem. But the leadfields computed using grads read with the old ctf
>> reader are only suitable for the 'raw' setting.
>>
>> Best,
>>
>> Vladimir
>>
>> On Wed, Jul 9, 2008 at 5:32 PM, Suresh Muthukumaraswamy
>> <sdmuthu at cardiff.ac.uk> wrote:
>> > Hi,
>> >  as far as I am aware fieldtrip reads in whatever gradiometer definition your data is saved as and
>> > doesnt apply any other processing to this
>> > You can check what the gradiometer definition of the saved data is  in DataEditor.
>> > In the Acq software you can pick what type of gradiometers the data is saved as. We usually just
>> > save it as 3rd order in the data at the Acq level and you dont have to worry about it from then on
>> > (unless you had some reason to undo the 3rd order gradiometers)
>> > - Suresh
>> >
>> > Suresh Muthukumaraswamy, PhD
>> > CUBRIC
>> > Cardiff University
>> > Park Place
>> > Cardiff, CF10 3AT
>> > United Kingdom
>> > email: sdmuthu at cardiff.ac.uk
>> > Phone: +44 (0)29 2087 0353
>> >
>> >>>> Cristiano Micheli <michelic72 at GMAIL.COM> 09/07/2008 17:02 >>>
>> > Hi All
>> > CTF software allows to open a MEG dataset and to apply a theoretical 3rd
>> > order gradiometers data correction, which makes use of a number of
>> > coefficients to correct raw data from common mode artifacts.
>> > Does Fieldtrip take in account this correction as well?
>> > Where is it coded?
>> > Regards
>> > Cristiano
>> >
>> > ----------------------------------
>> > 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/fcdonders/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/fcdonders/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/fcdonders/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/fcdonders/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/fcdonders/fieldtrip.



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