Hi Everyone,
Sorry to beat this topic to death, but I noticed a potential bug in MF 2.1 when performing the "dummy" autobad runs.  No matter what one sets the badlimit at, it never finds a bad channel (according to the log).  I have tried various values from 30 to 0.1 and never had a bad channel occurrence.  I have used several different raw.fif files, each about 5 mins at 1kHz.  Anyone else have this problem?

Maybe my data is just that good! (hehe)


On Fri, Oct 2, 2009 at 7:58 AM, Daniel Wakeman <[log in to unmask]> wrote:
Hi Tony,

The current version of MNE i.e. 2.6.0 will allow you to browse raw maxshield data see section 4.2.2 for more details (--allowmaxshield).


Tony W. Wilson wrote:
Matti and Yury,
Thanks again for the input.  I believe the 'dummy' MF pass is the way to go.  I cannot open/browse the raw file in ENM or MNE without some pass through MF because we use active shielding (smartshield) for all acquisitions.  Our room is only a 1-layer and our environment is quite noisy.  On a related note, is there any data (or opinions) on the degree to which bad channels affects MF performance (normal or tsss)?  I presume that including only one or two clearly bad channels would affect the accuracy of the MF results at least moderately, but maybe not.


On Fri, Oct 2, 2009 at 6:22 AM, Yury Shtyrov <[log in to unmask] <mailto:[log in to unmask]>> wrote:

   I think the new MF 2.1 should recognise MNE marking as well as ENM
   one (at least it was promised at some point) , but I have not had a
   chance to test this.

   In mark_bad_fiff you just specify a list of channels that you don't
   like, it does not do any detection itself. You can use mne_browse_raw
   or anything else (that can show raw data) to look through the channels
   to see which ones are bad, or do a 'dummy' pass of plain MF without
   tsss and see which ones are detected by autobad.


   2009/10/2 Matti Hamalainen <[log in to unmask]
   <mailto:[log in to unmask]>>:

    > Hi Tony,
    >does not involve any criteria. It just marks channels bad
    > irrespective of whether they really are bad or not.
    > As a side not, the MNE software employs a different way to mark
   channels bad
    > in a fif file. MNE for sure does not recognize the bad channel
   markings made
    > with mark_bad_fiff and I think Neuromag software does not
   recognize the bad
    > channels indicated by mne_mark_bad_channels.
    > - Matti
    > On Oct 1, 2009, at 3:08 PM, Tony W. Wilson wrote:
    > Thanks Yury.
    > Do you know how mark_bad_fiff defines a bad channel?  Is it the same
    > criteria described in the manual for the autobad feature?
    > Tony
    > On Thu, Oct 1, 2009 at 9:47 AM, Yury Shtyrov
    > <[log in to unmask]
   <mailto:[log in to unmask]>> wrote:
    >> This is certainly something that many people are doing in the
    >> version of MF here, and I can't see why you wouldn't do it in MF
    >> It's indeed either mark_bad_fiff or by entering them as bad channels
    >> using MF command line options.
    >> yury
    >> 2009/10/1 Tony W. Wilson <[log in to unmask]
   <mailto:[log in to unmask]>>:

    >> > I have been confused about whether Maxfilter 2.1 is excluding bad
    >> > channels
    >> > prior to computing the tsss correction.  I understand from
   watching the
    >> > program and reading the manual (Oct 2008 revision) that tsss
    >> > off
    >> > the automated bad channel detection, but does detect and exclude
    >> > saturated
    >> > channels and static bad channels from the computation.  To me,
   it seems
    >> > there could be additional channels one would want to exclude.  For
    >> > example,
    >> > sensors that were noisy in a particular run, or on that day,
   but were
    >> > not
    >> > excluded during acquisition (due to an oversight or whatever).  To
    >> > ensure
    >> > such channels are excluded, I'm guessing one needs to run
    >> > on
    >> > each raw file prior to tsss.  Is my understanding correct?  Is
    >> > else
    >> > doing this (ie., mark_bad_fiff, then tsss)?
    >> > All the best,
    >> > Tony
    >> > ___________________________________________________
    >> Yury Shtyrov, Dr.Phil., Prof.
    >> Senior Scientist (PLT)
    >> Manager, MEG Laboratory
    >> Medical Research Council (MRC)
    >> Cognition and Brain Sciences Unit
    >> 15 Chaucer Rd, CB2 7EF
    >> Cambridge, United Kingdom
    >> tel +44 1223 273703 (office)
    >> tel +44 1223 355294 (reception), ext 832
    >> fax +44 1223 359062
    >> e-mail [log in to unmask]
   <mailto:[log in to unmask]>

    >> http://www.mrc-cbu.cam.ac.uk/~yury
    > ---------
    > Matti Hamalainen, Ph.D.
    > Athinoula A. Martinos Center for Biomedical Imaging
    > Massachusetts General Hospital
    > [log in to unmask] <mailto:[log in to unmask]>

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