AW: [FIELDTRIP] AW: [FIELDTRIP] ft_channelrepair with neuromag data

David Ziegler daz at MIT.EDU
Wed Oct 27 17:40:12 CEST 2010


Thanks, Nina, for the link and in advance for anything you find out from
Neuromag support.  Did you use a similar command as mine?

Cheers!
David


On 10/27/2010 11:26 AM, Nina Kahlbrock wrote:
>
> Hi David,
>
> the link for the neuromeg discussion list is:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=NEUROMEG
>
> I am currently discussing those problems with the Elekta Neuromag
> support. I will let you know as soon as this has come to a conclusion.
>
> Cheers,
>
> Nina
>
> ------------------------------------------------------------------------
>
> *Von:*FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] *Im
> Auftrag von *David Ziegler
> *Gesendet:* Mittwoch, 27. Oktober 2010 17:02
> *An:* FIELDTRIP at NIC.SURFNET.NL
> *Betreff:* Re: [FIELDTRIP] AW: [FIELDTRIP] ft_channelrepair with
> neuromag data
>
> 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
>
>
> -----Urspr√ľngliche 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 <mailto: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> <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>
> <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>
>
> ---------------------------------------------------------------------------
> 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.
> ---------------------------------------------------------------------------
>
> ---------------------------------------------------------------------------
> 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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