preprocessing cleanup

Robert Oostenveld r.oostenveld at FCDONDERS.KUN.NL
Thu Aug 19 12:35:57 CEST 2004

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 Oostenveld, PhD
Center for Sensory-Motor Interaction (SMI)
Aalborg University, Denmark


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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