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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)

Thanks
Tony


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).
>
> Dan
>
> 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.
>>
>> Tony
>>
>> 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.
>>
>>    y.
>>
>>
>>    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
>>    previous
>>     >> version of MF here, and I can't see why you wouldn't do it in MF
>>    2.1.
>>     >> 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
>>    switches
>>     >> > 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
>>    mark_bad_fiff
>>     >> > on
>>     >> > each raw file prior to tsss.  Is my understanding correct?  Is
>>    anyone
>>     >> > 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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