preprocessing cleanup

[Robert Oostenveld]

Hi Christian,

Rereferencing for EEG data will certainly remain included.
My suggestion would be to implement rereferencing as a general option,
i.e.
     cfg.implicitref
     cfg.refchannel
     cfg.reref
would apply to all channels that are listed in cfg.channel, and
cfg.eegchannel would be obsoleted. This does mean that people in
principle could also apply nonsense rereferencing to MEG channels, but
if they are that stupid...

Robert

On 19 Aug 2004, at 13:06, christian forkstam wrote:

> 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'
>
> ...christian
> (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
>>
----------------------------------------------------------------------
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