preprocessing cleanup

christian forkstam christian.forkstam at FCDONDERS.KUN.NL
Thu Aug 19 13:06:15 CEST 2004

hey master fieldtripper,

if i understand the proposed modification correctly it seems like a
perfect idea to me. just to make sure i don't loose the possibility to
rereference my EEG data i just want to secure this option. as far as i
understan it does not hurt to include the possibility for both
MEG/EEG/EMG analysis but you know that better.

the options of concern:

%   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'

(soon out tripping the fields of a nothern swedish mountain area...)

Robert Oostenveld wrote:
> 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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