Hello Rik,
The reason fro skipping autobad with '-st' is simply to save time,
because '-st' (i.e. tSSS method) repeats the same work:
reconstructs the signals and inspects the residuals between
measured and predicted signals. Thus, any artifact waveforms in bad
channels are automatically captured and projected out by tSSS.
However, channels with higher white noise levels or showing
infrequent spiking-type artifacts are difficult to catch by autobad or tSSS
and they may need to be identified and set manually as bads.
You can run the program with autobad first, and try to catch
and set the bad channels e.g. via scripting. In my experience this path
does however not affect the tSSS outcome very much.
I would still recommend to inspect both input and output data (e.g. quick
visual screening in graph) to judge the quality.
Version 2.1 has a possibility to write the tSSS waveforms to an
evoked FIFF file and view them in xplotter (or in graph). Please see
the User's Guide (/neuro/manuals/MaxFilter-2.1.pdf) section 3.5 for
details.
In version 2.1, continuous HPI does not affect autobad scanning because
the autobad routine copies the data to a temporary buffer and performs
band-pass filtering to this copy before doing the detection.
Best regards, Jukka
Rik Henson wrote:
> Dear Neuromag -
>
> MaxFilter2.1 turns off automatic detection of bad channels (-autobad)
> when the MaxST (-st) option is selected (Section 3.5 of Manual). Is
> there a theoretical reason for this - ie, would it improve results if
> autobad were run first without st, and then any bad channels that were
> found passed as static bad channels (-bad) to a second run with st now
> active? (Also, does -autobad now work fine if continuous HPI was active
> during recording?)
>
> Thanks
> Rik
>
--
================================
Dr. Jukka Nenonen
Manager, Method development
Elekta Oy
Street address: Siltasaarenkatu 18-20A, Helsinki, Finland
Mailing address: P.O. Box 34, FIN-00531 HELSINKI, Finland
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+358 9 756 240 11 (fax), +358 9 756 2400 (operator)
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