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

Nina Kahlbrock Nina.Kahlbrock at UNI-DUESSELDORF.DE
Wed Oct 27 17:26:34 CEST 2010


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 
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> 

  

  


      

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--------------------------------------------------------------------------- 
  

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 


    

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

    

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-- 



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

 

 

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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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