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Hi Burkdard and Nina,<br>
<br>
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:<br>
<br>
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
<br>
<br>
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. <br>
<br>
Thanks!<br>
David<br>
<br>
<br>
On 10/26/2010 4:46 AM, Burkhard Maess wrote:
<blockquote cite="mid:4CC69576.5090501@cbs.mpg.de" type="cite">Dear
Nina,
<br>
<br>
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.
<br>
<br>
best wishes,
<br>
Burkhard
<br>
<br>
<br>
<br>
Nina Kahlbrock wrote:
<br>
<blockquote type="cite">Dear Burkhard,
<br>
I am also working on NM306 data and I have a specific problem
repairing
<br>
broken channels using maxfilter. This email might thus be more
suited for
<br>
the neuromeg discussion list. However, I thought it might be of
interest to
<br>
other NM users as well...
<br>
What I would like to do is pretty much the same as described in
the previous
<br>
mails: interpolate broken channels and use a standard head
position for
<br>
multiple recordings in one subject.
<br>
I used fieldtrip's automatic and semi-automatic artifact
rejection routines
<br>
to identify channels that are flat, show jumps and are noisy. I
defined
<br>
these as bad in maxfilter. Then I used sss/tsss to achieve the
desired
<br>
steps. It seemed very straight forward. However, when looking at
the results, the signal seems to be increased (and
<br>
more noisy and jumpy) in certain channels (see attached pdfs of
bad and
<br>
non-bad channel (1st page: raw data, 2nd page: sss data, 3rd
page: tsss
<br>
data). Have you ever experienced anything like this? The only
reason I can
<br>
come up with is that in maxfilter I used the continuous raw data
file and
<br>
not as in fieldtrip, only trials. Between trials there are
pauses, where the
<br>
channels could have been affected by a few movements. Could this
explain my
<br>
difficulties?
<br>
Is there a way to 'only' interpolate channels and realign the
head, without
<br>
impacting other non-broken channels?
<br>
Thank you very much for your answer!
<br>
Nina <br>
<br>
<br>
-----Ursprüngliche Nachricht-----
<br>
Von: FieldTrip discussion list [<a class="moz-txt-link-freetext" href="mailto:FIELDTRIP@NIC.SURFNET.NL">mailto:FIELDTRIP@NIC.SURFNET.NL</a>]
Im Auftrag
<br>
von Burkhard Maess
<br>
Gesendet: Freitag, 22. Oktober 2010 09:25
<br>
An: <a class="moz-txt-link-abbreviated" href="mailto:FIELDTRIP@NIC.SURFNET.NL">FIELDTRIP@NIC.SURFNET.NL</a>
<br>
Betreff: Re: [FIELDTRIP] ft_channelrepair with neuromag data
<br>
<br>
Dear David,
<br>
<br>
I agree with Jan-Mathijs.
<br>
<br>
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.
<br>
<br>
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.
<br>
<br>
all the best,
<br>
Burkhard
<br>
<br>
<br>
jan-mathijs schoffelen wrote:
<br>
<blockquote type="cite">Dear David,
<br>
<br>
This is a good point. As far as I can see from the code, no
distinction is made between gradiometers and magnetometers.
<br>
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.
<br>
<br>
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
<a class="moz-txt-link-freetext" href="http://fieldtrip.fcdonders.nl/example/megrealign">http://fieldtrip.fcdonders.nl/example/megrealign</a>.
<br>
<br>
Just out of curiosity: doesn't the maxfilter in the Neuromag
software allow for similar things?
<br>
<br>
Best wishes,
<br>
<br>
Jan-Mathijs <br>
On Oct 21, 2010, at 9:49 PM, David Ziegler wrote:
<br>
<br>
<blockquote type="cite">Hi Fieldtrippers,
<br>
<br>
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). <br>
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)?
<br>
<br>
Thanks!
<br>
David
<br>
<br>
-- <br>
David A. Ziegler
<br>
Department of Brain and Cognitive Sciences Massachusetts
Institute of Technology 43 Vassar St, 46-5121 Cambridge,
MA 02139
<br>
Tel: 617-258-0765
<br>
Fax: 617-253-1504
<br>
<a class="moz-txt-link-abbreviated" href="mailto:daz@mit.edu">daz@mit.edu</a> <a class="moz-txt-link-rfc2396E" href="mailto:daz@mit.edu"><mailto:daz@mit.edu></a>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
</blockquote>
</blockquote>
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<br>
<blockquote type="cite">Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour, Centre
for Cognitive Neuroimaging,
<br>
Radboud University Nijmegen, The Netherlands
<br>
<a class="moz-txt-link-abbreviated" href="mailto:J.Schoffelen@donders.ru.nl">J.Schoffelen@donders.ru.nl</a>
<a class="moz-txt-link-rfc2396E" href="mailto:J.Schoffelen@donders.ru.nl"><mailto:J.Schoffelen@donders.ru.nl></a>
<br>
Telephone: 0031-24-3614793
<br>
<br>
<br>
</blockquote>
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<p class="MsoNormal"><span style="font-size: 11pt;
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A. Ziegler<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Bodoni MT";">Department
of Brain and Cognitive Sciences <br>
Massachusetts Institute of Technology <br>
<st1:street w:st="on"><st1:address w:st="on">43
Vassar St</st1:address></st1:street><span
class="GramE">,<span style=""> </span>46</span>-5121
<br>
<st1:place w:st="on"><st1:city w:st="on">Cambridge</st1:city>,
<st1:state w:st="on">MA</st1:state> <st1:postalcode
w:st="on">02139</st1:postalcode></st1:place><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt;
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617-258-0765<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt;
font-family: "Bodoni MT";">Fax:
617-253-1504<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size: 11pt;
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