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NEUROMEG  October 2009

NEUROMEG October 2009

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Subject:

Re: Bad channel scans and tsss (MaxFilter 2.1)

From:

Yury Shtyrov <[log in to unmask]>

Reply-To:

Yury Shtyrov <[log in to unmask]>

Date:

Mon, 5 Oct 2009 18:01:21 +0400

Content-Type:

text/plain

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text/plain (182 lines)

We haven't had this in MF 2, I believe, it normally finds too many bad
channels. New version - new bugs? ;)

yury

2009/10/3 Tony W. Wilson <[log in to unmask]>:
> 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]>
>>>
>>>
>>
>>
>> --
>> BEGIN:VCARD
>> VERSION:3.0
>> N:Wakeman;Daniel;Gary;;
>> FN:Daniel Gary Wakeman
>> ORG:University of Cambridge;
>> TITLE:Student 2010
>> EMAIL;type=INTERNET;type=WORK;type=pref:[log in to unmask]
>> EMAIL;type=INTERNET;type=HOME:[log in to unmask]
>> item1.EMAIL;type=INTERNET:[log in to unmask]
>> item1.X-ABLabel:_$!<Other>!$_
>> TEL;type=WORK;type=pref:+44 (0) 1223 355 294 ex. 595
>> TEL;type=CELL:+44 (0) 7877 043 797
>> item2.TEL:+1 518-291-4347
>> item2.X-ABLabel:US
>> TEL;type=WORK;type=FAX:+44 (0) 1223 359 062
>> item3.ADR;type=HOME;type=pref:;;Wolfson College\nBarton
>> Road;Cambridge;Cambridgshire;CB3 9BB;United Kingdom
>> item3.X-ABADR:us
>> item4.X-AIM;type=pref:[log in to unmask]
>> item4.X-ABLabel:Video
>> X-AIM;type=HOME:WakerCrzy0
>> X-ABUID:F98E7710-43F5-4D9A-992F-E4FD6FFE5B6B\:ABPerson
>> END:VCARD
>
>

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