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).
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.
On Fri, Oct 2, 2009 at 6:22 AM, Yury Shtyrov <[log in to unmask] <mailto:[log in to unmask]>> wrote:<mailto:[log in to unmask]>>:
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.
2009/10/2 Matti Hamalainen <[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
> in a fif file. MNE for sure does not recognize the bad channel
> 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?
> On Thu, Oct 1, 2009 at 9:47 AM, Yury Shtyrov
> <[log in to unmask]<mailto:[log in to unmask]>> wrote:<mailto:[log in to unmask]>>:
>> This is certainly something that many people are doing in the
>> version of MF here, and I can't see why you wouldn't do it in MF
>> It's indeed either mark_bad_fiff or by entering them as bad channels
>> using MF command line options.
>> 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
>> > program and reading the manual (Oct 2008 revision) that tsss
>> > off
>> > the automated bad channel detection, but does detect and exclude
>> > saturated
>> > channels and static bad channels from the computation. To me,
>> > there could be additional channels one would want to exclude. For
>> > example,
>> > sensors that were noisy in a particular run, or on that day,
>> > not
>> > excluded during acquisition (due to an oversight or whatever). To
>> > ensure
>> > such channels are excluded, I'm guessing one needs to run
>> > on
>> > each raw file prior to tsss. Is my understanding correct? Is
>> > 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]> [log in to unmask] <mailto:[log in to unmask]>
> Matti Hamalainen, Ph.D.
> Athinoula A. Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
FN:Daniel Gary Wakeman
ORG:University of Cambridge;
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