preprocessing cleanup

Pascal Fries Pascal.Fries at FCDONDERS.KUN.NL
Thu Aug 19 12:41:46 CEST 2004

Hi Robert,

 I suggest that we discuss this at the fieldtrip meeting.

Best, Pascal

> -----Original Message-----
> From: FieldTrip discussion list
> [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Robert Oostenveld
> Sent: Thursday, August 19, 2004 12:36 PM
> Subject: [FIELDTRIP] preprocessing cleanup
> Dear FieldTrippers,
> Related to the upcoming release of FieldTrip, I am busy
> cleaning up parts of the code that are not so clear at the
> moment. One of them is preprocessing and definetrial.
> Currently the preprocessing function is reading multiple
> datatypes at once and giving each of them a different
> treatment. This clearly reflects that preprocessing was
> initially written for MEG data and that other dataformats
> were added later.
> Specifically, these two sections in the help of preprocessing
> are what bothers me.
> % Specific preprocessing options for EMG channels are
> %   cfg.emgchannel  = cell-array with the label(s) of EMG channels
> %   cfg.emghpfreq   = high-pass frequency
> %   cfg.emgrectify  = 'yes' or 'no'
> %   cfg.emghilbert  = 'yes' or 'no'
> %
> % Specific preprocessing options for EEG channels are
> %   cfg.eegchannel  = cell-array with the label(s) of EEG channels
> %   cfg.implicitref = 'label' or empty, add the implicit reference as
> zeros prior to rereferencing
> %   cfg.refchannel  = cell-array with new reference channel(s)
> %   cfg.reref       = 'no' or 'yes'
> All other preprocessing options are applied to MEG as well as
> to EMG and EOG channel groups, which means that you currently
> can NOT apply different filter settings for EMG and MEG
> channels, or apply baseline correction to only one of them.
> I would like to suggest the following changes
>    1) there will be no MEG/EEG/EMG specific options any more
>    2) preprocessing will treat all channels the same
>    3) if you want to apply different settings to different
> channel groups (e.g. to the MEG and the EEG channels), you
> should call preprocessing twice and concatenate the resulting
> raw data objects.
> These changes will facilitate further improvements of the
> preprocessing function, as well of the artifact detection
> routines. Regarding item 3:
> I can of course explain how to do it (or I could even write a
> general function for that). Important for item 3 is that it
> will not be neccessary to redo the artifact detection
> multiple times for the different channel groups that you want
> to concatenate.
> I would like to get your feedback on the following two items:
> At the moment I am only aware of Jan-Mathijs mixing different
> channel groups in his analyses, so please let me know if you
> are also using EMG and/or EEG channels and their specific
> preprocessing options. Furthermore, if you have particular
> opinions about this issue, let me know as soon as ppossible
> (either to me directly, through the fieldtrip list or at the
> thursday MEG meeting). If I don't get any objections, I will
> implement the changes as suggested.
> best regards,
> Robert
> ----------------------------------------------------------------------
> Robert Oostenveld, PhD
> Center for Sensory-Motor Interaction (SMI) Aalborg University, Denmark
> and
> F.C. Donders Centre for Cognitive Neuroimaging University
> Nijmegen P.O. Box 9101 NL-6500 AH Nijmegen The Netherlands
> Tel: +31 (0)24 3619695
> Fax: +31 (0)24 3610989

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