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
-----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> <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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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.
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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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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.
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You are receiving this message because you are subscribed to
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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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