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<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Hi David, <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>the link for the neuromeg
discussion list is: <a
href="https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=NEUROMEG">https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=NEUROMEG</a><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Cheers, <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Nina<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
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<p class=MsoNormal><b><font size=2 color=black face=Tahoma><span
style='font-size:10.0pt;font-family:Tahoma;color:windowtext;font-weight:bold'>Von:</span></font></b><font
size=2 color=black face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;
color:windowtext'> <st1:PersonName w:st="on">FieldTrip discussion list</st1:PersonName>
[mailto:FIELDTRIP@NIC.SURFNET.NL] <b><span style='font-weight:bold'>Im Auftrag
von </span></b>David Ziegler<br>
<b><span style='font-weight:bold'>Gesendet:</span></b> Mittwoch, 27. Oktober
2010 17:02<br>
<b><span style='font-weight:bold'>An:</span></b> FIELDTRIP@NIC.SURFNET.NL<br>
<b><span style='font-weight:bold'>Betreff:</span></b> Re: [FIELDTRIP] AW:
[FIELDTRIP] ft_channelrepair with neuromag data</span></font><font color=black><span
style='color:windowtext'><o:p></o:p></span></font></p>
</div>
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style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'>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: <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'>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>
<br>
<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'>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: <st1:PersonName w:st="on">FieldTrip discussion list</st1:PersonName> [<a
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 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>
<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'>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
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>
<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'>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 href="mailto:daz@mit.edu">daz@mit.edu</a> <a href="mailto:daz@mit.edu"><mailto:daz@mit.edu></a>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<o:p></o:p></span></font></p>
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style='font-size:12.0pt'>---------------------------------------------------------------------------
<o:p></o:p></span></font></p>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt' type=cite>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'>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 <a
href="http://listserv.surfnet.nl/archives/fieldtrip.html">http://listserv.surfnet.nl/archives/fieldtrip.html</a>
and <a href="http://www.ru.nl/neuroimaging/fieldtrip">http://www.ru.nl/neuroimaging/fieldtrip</a>.
<br>
<br>
<o:p></o:p></span></font></p>
</blockquote>
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style='font-size:12.0pt'>---------------------------------------------------------------------------
<br>
<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
style='font-size:12.0pt'>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 href="mailto:J.Schoffelen@donders.ru.nl">J.Schoffelen@donders.ru.nl</a> <a
href="mailto:J.Schoffelen@donders.ru.nl"><mailto:J.Schoffelen@donders.ru.nl></a>
<br>
Telephone: 0031-24-3614793 <br>
<br>
<br>
<o:p></o:p></span></font></p>
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style='font-size:12.0pt'>---------------------------------------------------------------------------
<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=black face="Times New Roman"><span
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and <a href="http://www.ru.nl/neuroimaging/fieldtrip">http://www.ru.nl/neuroimaging/fieldtrip</a>.
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<o:p></o:p></span></font></p>
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<p class=MsoNormal><font size=2 color=black face="Bodoni MT"><span
style='font-size:11.0pt;font-family:"Bodoni MT"'>David A. Ziegler<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=black face="Bodoni MT"><span
style='font-size:11.0pt;font-family:"Bodoni MT"'>Department of Brain and
Cognitive Sciences <br>
Massachusetts Institute of Technology <br>
<st1:street u6:st="on"><st1:address u6:st="on">43 Vassar St</st1:address></st1:street>,
46-5121 <br>
<st1:place u6:st="on"><st1:city u6:st="on">Cambridge</st1:city>, <st1:state u6:st="on">MA</st1:state>
<st1:postalcode u6:st="on">02139</st1:postalcode></st1:place><u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=black face="Bodoni MT"><span
style='font-size:11.0pt;font-family:"Bodoni MT"'>Tel: 617-258-0765<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=black face="Bodoni MT"><span
style='font-size:11.0pt;font-family:"Bodoni MT"'>Fax: 617-253-1504<u1:p></u1:p></span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=black face="Bodoni MT"><span
style='font-size:11.0pt;font-family:"Bodoni MT"'><a href="mailto:daz@mit.edu">daz@mit.edu</a><u1:p></u1:p></span></font><o:p></o:p></p>
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You are receiving this message because you are subscribed to <br>
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