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]> 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.


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
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