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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]> 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]>:
>
> 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]> 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]>:
>> > 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]
>> 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]