forming one datset from multiple data files

[jan-mathijs schoffelen]

Dear David,

The reason why the sensor info is explicitly removed by ft_appenddata
is to ensure that people realize that combining multiple sessions may
be problematic or even downright 'forbidden' for some subsequent steps
in the analysis. Think of e.g. doing source analysis for a single
subject in which several sessions are combined. Since the subject's
position was slightly different during each recording sessions, there
is in fact not a guarantee that during one of the sessions the subject
would have sat facing backwards ;o). The leadfields computed in such a
case (appending with in one of the sessions the subject facing
backwards) will clearly be wrong for most of the data. Of course if
you were able to somehow compensate for the differences in position,
e.g. by applying the maxfilter, things may be different.
Yet, indeed for visualizing the results, and if you are confident that
there were no gross differences across the sessions with respect to
the positioning of the subject, there is no objection against keeping
the gradiometer info. Although I am a bit puzzled by the fact that you
do not seem to be able to visualize the data as you have it (because I
thought that provided you give the plotting function an appropriate
layout-file, in your case something like NM306xxx.lay, I would assume
that it just works even without sensor position info; for the layout
files, have a look in fieldtrip/templates, or at the wiki), you could
of course 'fool' fieldtrip by appending a grad-structure to your
concatenated data: allT4.grad = dataT4_list1.grad;

Hope this helps,
Jan-Mathijs


On Apr 14, 2010, at 9:19 PM, David Ziegler wrote:

> Hi Fieldtrippers,
>
> I have a similar situation where I have 3 "runs" of trials that were
> collected separately on a neuromag306 system.  I took Ingrid's
> advice and
> ran ft_appenddata on my preprocessed (e.g., trigger-based trial
> selection,
> artifact rejection, and preprocessing) data files to combine the three
> datasets into a single file.  The function worked, but with the
> warning that
> the sensor info was not consistent across trials:
>
>>> cfg=[];
>>> allT4 = ft_appenddata(cfg, dataT4_list11, dataT4_list8,
>>> dataT4_list9);
> input dataset 1, 308 channels, 32 trials
> input dataset 2, 308 channels, 32 trials
> input dataset 3, 308 channels, 32 trials
> Warning: sensor information does not seem to be consistent across
> the input
> arguments
>> In ft_appenddata at 106
> concatenating the trials over all datasets
> removing sensor information from output
> output dataset, 308 channels, 96 trials
>
> Is there a better way to concatenate several runs of similar trials
> such
> that the sensor information is preserved?  I can generate an time-
> locked
> average on the resulting concatenated data, but I am not able to
> plot it
> using multiplot or topoplot, just by viewing individual single
> channels
> (presumably due to the stripping of the sensory info).
>
> Thanks for any advice!
> David
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>  and http://www.ru.nl/neuroimaging/fieldtrip.
>

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3668063

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.