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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