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<font face="Georgia">Thanks, Nina, for the link and in advance for
anything you find out from Neuromag support. Did you use a
similar command as mine? <br>
<br>
Cheers!<br>
David<br>
<br>
</font><br>
On 10/27/2010 11:26 AM, Nina Kahlbrock wrote:
<blockquote cite="mid:000a01cb75eb$573904b0$cd136386@VMED.UKD"
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<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color:
navy;" lang="EN-GB">Hi David, <o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color:
navy;" lang="EN-GB">the link for the neuromeg
discussion list is: <a moz-do-not-send="true"
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 color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color:
navy;" lang="EN-GB">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 color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color:
navy;" lang="EN-GB">Cheers, <o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color:
navy;" lang="EN-GB">Nina<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color:
navy;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color:
navy;" lang="EN-GB"><o:p> </o:p></span></font></p>
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<p class="MsoNormal"><b><font color="black" face="Tahoma"
size="2"><span style="font-size: 10pt; font-family:
Tahoma; color: windowtext; font-weight: bold;">Von:</span></font></b><font
color="black" face="Tahoma" size="2"><span
style="font-size: 10pt; font-family: Tahoma; color:
windowtext;"> <st1:personname w:st="on">FieldTrip
discussion list</st1:personname>
[<a class="moz-txt-link-freetext" href="mailto:FIELDTRIP@NIC.SURFNET.NL">mailto:FIELDTRIP@NIC.SURFNET.NL</a>] <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>
<a class="moz-txt-link-abbreviated" href="mailto:FIELDTRIP@NIC.SURFNET.NL">FIELDTRIP@NIC.SURFNET.NL</a><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>
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<p class="MsoNormal"><font color="black" face="Times New
Roman" size="3"><span style="font-size: 12pt;">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 color="black" face="Times New
Roman" size="3"><span style="font-size: 12pt;">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 color="black" face="Times New
Roman" size="3"><span style="font-size: 12pt;">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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 color="black" face="Times New
Roman" size="3"><span style="font-size: 12pt;">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 moz-do-not-send="true"
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 color="black" face="Times New
Roman" size="3"><span style="font-size: 12pt;">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 moz-do-not-send="true" href="mailto:daz@mit.edu">daz@mit.edu</a>
<a moz-do-not-send="true" 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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<o:p></o:p></span></font></p>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;"
type="cite">
<p class="MsoNormal"><font color="black" face="Times New
Roman" size="3"><span style="font-size: 12pt;">You are
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share experiences and to
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moz-do-not-send="true"
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<br>
<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Times New
Roman" size="3"><span style="font-size: 12pt;">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 moz-do-not-send="true"
href="mailto:J.Schoffelen@donders.ru.nl">J.Schoffelen@donders.ru.nl</a>
<a moz-do-not-send="true"
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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Roman" size="3"><span style="font-size: 12pt;">---------------------------------------------------------------------------
<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Times New
Roman" size="3"><span style="font-size: 12pt;">You are
receiving this message because you are
subscribed to <br>
the FieldTrip list. The aim of this list is to
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experiences <br>
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See also <a moz-do-not-send="true"
href="http://listserv.surfnet.nl/archives/fieldtrip.html">http://listserv.surfnet.nl/archives/fieldtrip.html</a>
<br>
and <a moz-do-not-send="true"
href="http://www.ru.nl/neuroimaging/fieldtrip">http://www.ru.nl/neuroimaging/fieldtrip</a>.
<br>
<br>
<o:p></o:p></span></font></p>
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<p class="MsoNormal"><font color="black"
face="Bodoni MT" size="2"><span
style="font-size: 11pt; font-family:
"Bodoni MT";">David A. Ziegler<u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black"
face="Bodoni MT" size="2"><span
style="font-size: 11pt; 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 color="black"
face="Bodoni MT" size="2"><span
style="font-size: 11pt; font-family:
"Bodoni MT";">Tel: 617-258-0765<u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black"
face="Bodoni MT" size="2"><span
style="font-size: 11pt; font-family:
"Bodoni MT";">Fax: 617-253-1504<u1:p></u1:p></span></font><o:p></o:p></p>
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style="font-size: 11pt; font-family:
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See also <a class="moz-txt-link-freetext" href="http://listserv.surfnet.nl/archives/fieldtrip.html">http://listserv.surfnet.nl/archives/fieldtrip.html</a> <br>
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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
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<p class="MsoNormal"><span style="font-size: 11pt;
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617-258-0765<o:p></o:p></span></p>
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617-253-1504<o:p></o:p></span></p>
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<p>---------------------------------------------------------------------------
You are receiving this message because you are subscribed to <br>
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and to discuss new ideas for MEG and EEG analysis. <br>
See also http://listserv.surfnet.nl/archives/fieldtrip.html <br>
and http://www.ru.nl/neuroimaging/fieldtrip.<br>
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