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]