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= Avoid MaxFilter Bugs! =
CBU researchers have encountered problems using some options in Neuromag's Max Filter program, and in discussing these issues with the Neuromag software engineers, we have learned of a few other bugs too. These are briefly summarised below and will be expanded upon as we gain more info. See the "neuromeg" mailing list archives for the full discussion (and if you haven't done it already, join the list!): http://www.jiscmail.ac.uk/archives/neuromeg.html
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'''Don't use '-trans default' without setting '-frame' and '-origin'''' = MaxFilter =
A common first step in analysing your data is to pre-processing them using the Maxfilter program. This Neuromag sofware implements "Signal-Space Separation" (SSS), which is a clever mathematical way to separate magnetic signals coming from within the brain (or more precisely, a sphere within the sensors) from those coming from outside the brain (or more precisely, from outside a sphere outside the sensors). There are several technical papers on Maxfilter theory and application by Samu Taulu et al.
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If you attempt to transform the subject's head position to the 'default' position corresponding to the origin of the device coordinate frame (see p. 33 of Max Filter User's Guide) without specifying the -frame and -origin options, the transformed data will contain large-amplitude noise at the vertex. This bug is known to Neuromag and they are working on a solution. Apparently Max Move works ok when the target position is defined in another file, or with the default option when -frame and -origin are specified, e.g.: '-trans other_file_sss.fif' or '-trans default -frame head -origin 0 0 40' Maxfilter is essential if you have acquired your data using Maxshield (to remove the shielding effects). It is also helpful for 1) removing noise, particularly using its "temporal extension", 2) detecting bad channels, 3) realigning (interpolated) data after movement (provided you have used continuous HPI) and 4) moving the data to a standard space (e.g, across subjects).
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'''Don't use '-trans' with head-movement compensation '-movecomp'''' In the past, we have had Maxfilter versions 2.0 and 2.1 (see below); we now use version 2.2. You can find user manuals under the relevant versions of Maxfilter
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According to Neuromag, -movecomp always returns the head position to the '''initial''' position in the recording. See also the archives of this email list (www.jiscmail.ac.uk/lists/NEUROMEG.html‎) which you may also want to join to hear about latest maxfilter updates.
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'''Don't use '-autobad' with head-position estimation '-headpos' or movement compensation '-movecomp''''

Just don't. Apparently -autobad is fine alone (but not really recommended anyway), and -headpos and -movecomp are fine without -autobad. Instead of -autobad, it is recommended that you inspect your raw data, note any noisy or otherwise 'bad' sensors, and use the -bad <sensor number(s)>, e.g.: '-bad 521 1421 2413'''' '''

'''Don't use '-lpfilt' to low-pass filter data'''

According to Neuromag, -lpfilt uses an IIR filter which introduces a delay in the output signal. Note that downsampling, option -ds, also necessarily low-pass filters data but it does not cause the same delay because it uses an FIR filter.
 * [[Maxfilter_V2.2|Maxfilter 2.2]]
 * [[maxOlderVersions|Previous versions of Maxfilter (2.0/2.1)]]
 * [[maxCBURun|Running Maxfilter at CBU]]
 * [[maxoptions|Command line options]]
 * [[maxpreproc|Guideline(s) for data preprocessing]]
 * [[maxdiagnost|Maxfilter Output Diagnostics]]

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MaxFilter

A common first step in analysing your data is to pre-processing them using the Maxfilter program. This Neuromag sofware implements "Signal-Space Separation" (SSS), which is a clever mathematical way to separate magnetic signals coming from within the brain (or more precisely, a sphere within the sensors) from those coming from outside the brain (or more precisely, from outside a sphere outside the sensors). There are several technical papers on Maxfilter theory and application by Samu Taulu et al.

Maxfilter is essential if you have acquired your data using Maxshield (to remove the shielding effects). It is also helpful for 1) removing noise, particularly using its "temporal extension", 2) detecting bad channels, 3) realigning (interpolated) data after movement (provided you have used continuous HPI) and 4) moving the data to a standard space (e.g, across subjects).

In the past, we have had Maxfilter versions 2.0 and 2.1 (see below); we now use version 2.2. You can find user manuals under the relevant versions of Maxfilter

See also the archives of this email list (www.jiscmail.ac.uk/lists/NEUROMEG.html‎) which you may also want to join to hear about latest maxfilter updates.

CbuMeg: Maxfilter (last edited 2022-07-18 15:02:40 by OlafHauk)