CTF 3rd order gradiometers correction

Vladimir Litvak v.litvak at ION.UCL.AC.UK
Thu Jul 10 17:13:58 CEST 2008


What I understand from Robert is that the coefficients are not fixed.
They are at least site-specific if not file-specific. So the new way
should really be optimal. Guido, if you can also do some testing and
compare with your existing code, that'd be helpful.

Best,

Vladimir

On Thu, Jul 10, 2008 at 3:52 PM, Guido Nolte
<guido.nolte at first.fraunhofer.de> wrote:
> Guys,
> some years ago I stumbled over the same problem.
> I want to add to this discussion that it is
> quite important to properly include the 3rd-order
> gradiometer into the lead field. For a phantom
> experiment with a single dipole the error reduced by about a factor
> 10 as compared to simply ignoring that and treating
> the signals as simple gradiometer measurements (if I remember
> right).
> Back then I actually asked CTF for
> the coefficients (which they considered as a weird
> request (which I considered as weird)),
> and included that into my own programs.
> I still have these coefficients.
>
> Regards, Guido
>
>
> Vladimir Litvak wrote:
>>
>> 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.
>
> ----------------------------------
> 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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