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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