Hi,
Do you get the same problem when you use another fiff-file for -trans (rather than default)? For example, if you use the identical fiff-file, or one from the same subject but another session (if available)? This may allow you to determine whether the problem is the distance to the default sensor configuration, or something more fundamental. I would recommend using some "average sensor configuration" across subjects for -trans (see e.g. http://imaging.mrc-cbu.cam.ac.uk/meg/StandardSensorArray), in order to minimise extrapolation errors.
Olaf
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Olaf Hauk, PhD
MRC Cognition and Brain Sciences Unit
Phone: +44(0)1223 273702
Fax: +44(0)1223 359062
-----Original Message-----
From: Announcement for the Neuro MEG list [mailto:[log in to unmask]] On Behalf Of Zara Bergström
Sent: 28 October 2010 16:21
To: [log in to unmask]
Subject: Re: problem with maxfilter
Hi David and Neuromeg list,
I seem to have the same problem, although I get this for all my files. I run the -trans default step in a separate stage without any other concurrent processing as specified here:
http://imaging.mrc-cbu.cam.ac.uk/meg/maxpreproc
I have tried specifying the origin either as [0,0,40] or as the subject-specific origin from a previous sss while applying a small correction as recommended on the web page above. In all cases, the transform seems to redistribute almost all of the variance to a few channels, and wiping out signal at other channels. As an MEG newbie, I am unsure of whether this is the expected output or an error, but it looks kind of strange? Furthermore, the result looks the same with Maxfilter 2.1, which supposedly should have that particular bug fixed.
I have attached two figures which show average MEG magnetometer data with or without -trans (sorry I can't plot this topographically since the transform also strips the data of coordinates).
Any suggestions would be very much appreciated!
Thanks,
Zara
On Oct 28 2010, David Ziegler wrote:
>Hello Neuromeg users,
>
>I am having a problem running maxfilter 2.0 on my MEG data to
>auto-detect bad channels and transform each subject's head position. In
>about half of the cases, the results look good, but occasionally the
>resulting data seem to be noisier than the original data. I am aware of
>the known bug where using "-trans default" w/o specifying -frame and
>-origin results in noise at the vertex. This is exactly what I am
>seeing, but I did specify these two parameters in my command.
>
>I am attaching two figures, one with maxfiltering and one w/o (the data
>have been read into fieldtrip and I am displaying only the gradiometer
>data. also, the channels are plotted numerically, but the sensors with
>the noise tend to be close to the vertex). Does anyone have an idea as
>to what might be going on and what I can do to remedy the problem?
>
>The command I ran is:
>
>maxfilter -f $f_i{each subjects fif file} -origin 0 0 40 -frame head
>-autobad 30 -badlimit 7 -in 8 -out 3 -trans default
>
>Thanks!
>David
>
>
>
--
Dr Zara Bergström
Postdoctoral Research Associate
Behavioural and Clinical Neuroscience Institute and Department of Experimental Psychology University of Cambridge Downing Street Cambridge CB2 3EB UK
Tel: + 44 1223 333535
http://www.neuroscience.cam.ac.uk/directory/profile.php?zmb25
http://research.psychol.cam.ac.uk/~memlab/index.html
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