AW: [FIELDTRIP] ft_channelrepair with neuromag data

Wed Oct 27 17:01:46 CEST 2010

Hi Burkdard and Nina,

First off, thanks for the great advice Burkhard (and Jan-Mathijs).
Following your advice, I processed my raw neuromag data with maxfilter,
and I ended up with some results that are quite similar to what Nina is
seeing.  This doesn't happen for all of my subjects, but for about half
of them, I get increased noise in select channels following maxfilter.
I believe I used maxfilter v2.0 and my command line was:

maxfilter -f $f_i{each subject's fif file} -origin 0 0 40 -frame head
-autobad 30 -badlimit 7 -in 8 -out 3 -trans default

You mentioned that this should probably be posted to the neuromag list,
but I am not currently on that list and wasn't able to find it with a
quick search.  I'd be happy to repost there if you point me to the
sign-up page.

Thanks!
David

On 10/26/2010 4:46 AM, Burkhard Maess wrote:
> Dear Nina,
>
> indeed this looks funny. I have seen that maxfilter sometimes has
> produced unexpected results, but usually the channels have less noise
> after transformation. Your displays demonstrate the problem, but
> provide insufficient information to search for origin of it. I think,
> it is necessary to place one of these files to an ftp-server together
> with the list of bad channels you have used and the version of
> maxfilter. I would recommend to ask Jukka Nennonen for help because he
> is the maxfilter-pro and the displayed result should not show up. We
> shall continue the discussion here when we know the reason for this
> strange behavior.
>
> best wishes,
> Burkhard
>
>
>
> Nina Kahlbrock wrote:
>> Dear Burkhard,
>> I am also working on NM306 data and I have a specific problem repairing
>> broken channels using maxfilter. This email might thus be more suited
>> for
>> the neuromeg discussion list. However, I thought it might be of
>> interest to
>> other NM users as well...
>> What I would like to do is pretty much the same as described in the
>> previous
>> mails: interpolate broken channels and use a standard head position for
>> multiple recordings in one subject.
>> I used fieldtrip's automatic and semi-automatic artifact rejection
>> routines
>> to identify channels that are flat, show jumps and are noisy. I defined
>> these as bad in maxfilter. Then I used sss/tsss to achieve the desired
>> steps. It seemed very straight forward. However, when looking at the
>> results, the signal seems to be increased (and
>> more noisy and jumpy) in certain channels (see attached pdfs of bad and
>> non-bad channel (1st page: raw data, 2nd page: sss data, 3rd page: tsss
>> data). Have you ever experienced anything like this? The only reason
>> I can
>> come up with is that in maxfilter I used the continuous raw data file
>> and
>> not as in fieldtrip, only trials. Between trials there are pauses,
>> where the
>> channels could have been affected by a few movements. Could this
>> explain my
>> difficulties?
>> Is there a way to 'only' interpolate channels and realign the head,
>> without
>> impacting other non-broken channels?
>> Thank you very much for your answer!
>> Nina
>>
>>
>> -----Ursprüngliche Nachricht-----
>> Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im
>> Auftrag
>> von Burkhard Maess
>> Gesendet: Freitag, 22. Oktober 2010 09:25
>> An: FIELDTRIP at NIC.SURFNET.NL
>> Betreff: Re: [FIELDTRIP] ft_channelrepair with neuromag data
>>
>> Dear David,
>>
>> I agree with Jan-Mathijs.
>>
>> variant a: apply maxfilter - that will repair all broken channels.
>> You also can manually define certain channels as broken. Maxfilter
>> may also align data of different headpositions to a single position.
>>
>> variant b: use megrealign - it includes a minimum norm localization
>> and from there MEG data is forward computed. In this way, you can
>> repair channels, align different head positions to the same and even
>> convert data between different systems.
>>
>> all the best,
>> Burkhard
>>
>>
>> jan-mathijs schoffelen wrote:
>>> Dear David,
>>>
>>> This is a good point. As far as I can see from the code, no
>>> distinction is made between gradiometers and magnetometers.
>>> Naively, I would propose the following: first indeed split the data
>>> into two subset: gradiometers only and magnetometers only, only then
>>> apply the channel reparation routine. Yet, for the gradiometer
>>> subset data, it is questionable whether as such the replacement of a
>>> bad channel with its neighbours makes sense, because this would lead
>>> to averaging gradients of the magnetic field with an orthogonal
>>> orientation.
>>>
>>> In other words, this is probably not the most sensible approach. I
>>> don't think repairing after combining the planar gradients is
>>>  desired, because this leads to an unwanted amplification of the
>>> noise (because the combination step results in taking an absolute
>>> value). Alternatively, you could consider using ft_megrealign, which
>>> in principle could be used to repair bad channels. The recipe would
>>> be to only use the data with the clean channels in the input, and
>>> you would want to interpolate the data back onto the original
>>> sensor-array. An example for interpolating between two types of
>>> CTF-systems is shown here
>>> http://fieldtrip.fcdonders.nl/example/megrealign.
>>>
>>> Just out of curiosity: doesn't the maxfilter in the Neuromag
>>> software allow for similar things?
>>>
>>> Best wishes,
>>>
>>> Jan-Mathijs
>>> On Oct 21, 2010, at 9:49 PM, David Ziegler wrote:
>>>
>>>> Hi Fieldtrippers,
>>>>
>>>> I would like to use ft_channelrepair to interpolate data for some
>>>> missing/deleted channels with Neuromag 306 data.  I am just
>>>> wondering whether there are any potential problems with using the
>>>> nearest neighbor interpolation, given the triplet format of the
>>>> Neuromag system (two planar gradiometers and one magnetometer).
>>>> If this is problematic, are there other options to fixing
>>>> bad/missing channels (e.g., can ft_channelrepair be run on just a
>>>> subset of the channels, say the gradiometers after I run
>>>> ft_combineplanar)?
>>>>
>>>> Thanks!
>>>> David
>>>>
>>>> --
>>>> David A. Ziegler
>>>> Department of Brain and Cognitive Sciences Massachusetts Institute
>>>> of Technology 43 Vassar St,  46-5121 Cambridge, MA  02139
>>>> Tel: 617-258-0765
>>>> Fax: 617-253-1504
>>>> daz at mit.edu <mailto:daz at mit.edu>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>> ---------------------------------------------------------------------------
>>
>>>> You are receiving this message because you are subscribed to the
>>>> FieldTrip list. 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.
>>>>
>> ---------------------------------------------------------------------------
>>
>>> Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain,
>>> Cognition and Behaviour, Centre for Cognitive Neuroimaging,
>>> Radboud University Nijmegen, The Netherlands
>>> J.Schoffelen at donders.ru.nl <mailto:J.Schoffelen at donders.ru.nl>
>>> Telephone: 0031-24-3614793
>>>
>>>
>> ---------------------------------------------------------------------------
>>
>>> You are receiving this message because you are subscribed to
>>> the FieldTrip list. 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.
>>>
>> ---------------------------------------------------------------------------
>>
>>
>

--

David A. Ziegler

Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St,46-5121
Cambridge, MA 02139

Tel: 617-258-0765

Fax: 617-253-1504

daz at mit.edu <mailto:daz at mit.edu>

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See also http://listserv.surfnet.nl/archives/fieldtrip.html
and http://www.ru.nl/neuroimaging/fieldtrip.
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