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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 > >