[FieldTrip] plotting tutorial

[Schoffelen, J.M. (Jan Mathijs)]

Hi Mona,

I think that you first need to look into what you actually want to achieve. From the context of this thread it seems that you want to visualise data that has been collected with a ‘neuromag306’ MEG device, which is further supported by the fact that you mentioned having an ‘.fif’ file. However, you don’t mention whether you have read in actual data to-be-plotted. You only mention that you have read in the header information (as per ft_read_header). Using ft_read_data is not going to do the trick. In order to use the higher level plotting functions, you need to create a data object as per ft_preprocessing. Please refer to the tutorial documentation on http://www.fieldtriptoolbox.org/tutorial/natmeg/preprocessing/, for instance.

Jan-Mathijs


J.M.Schoffelen, MD PhD
Senior Researcher, VIDI-fellow - PI, language in interaction
Telephone: +31-24-3614793
Physical location: room 00.028
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands




Yes, I have tried the neuromag306all.lay and neuromag306cmb.lay.  My issue is I don’t know what format/data structure my data needs to be in order to use these layouts since the example neuromag306.mat was empty so didn’t work with the neuromag layouts.  I did read in my neuromag data using the ft_read_header() and ft_read_data() but not sure how to use it with the plotting function ft_multiplotER(), ft_topoplotER() and/or ft_topoplotTFR().

All help/tips are welcome

thanks,
Mona


On Feb 10, 2019, at 11:42 PM, Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen at donders.ru.nl<mailto:jan.schoffelen at donders.ru.nl>> wrote:

Hi Mona,

Have you tried the layout files that are contained in fieldtrip/template/layout.
I think that there should be a few that would suit your needs.

Best wishes,
Jan-Mathijs


J.M.Schoffelen, MD PhD
Senior Researcher, VIDI-fellow - PI, language in interaction
Telephone: +31-24-3614793
Physical location: room 00.028
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands



On 9 Feb 2019, at 03:33, Wong-Barnum, Mona <mona at sdsc.edu<mailto:mona at sdsc.edu>> wrote:


Hi:

I’m working my way through the plotting tutorial at http://www.fieldtriptoolbox.org/tutorial/plotting/.  I would like to use the neuromag306all.lay layout to plot the data.  I tried the neuromag306.mat from ftp but that didn’t work; it seems the data read in from neuromag306.mat doesn’t actually contain any data:

sens

sens =

 struct with fields:

   chanpos: [2x3 double]
   elecpos: [2x3 double]
     label: {2x1 cell}
      unit: ‘cm'


I have my own neuromag .fif file but not sure how to use the layout to plot my data (read in following the instructions at page http://www.fieldtriptoolbox.org/getting_started/neuromag/):

hdr

hdr =

 struct with fields:

         label: {389x1 cell}
        nChans: 389
            Fs: 603.1072
          grad: [1x1 struct]
          elec: [1x1 struct]
      nSamples: 192000
   nSamplesPre: 0
       nTrials: 1
          orig: [1x1 struct]
      chantype: {389x1 cell}
      chanunit: {389x1 cell}


All tips/help are appreciated.

thanks,
Mona

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    Mona Wong
    Web & iPad Application Developer
    San Diego Supercomputer Center

    "I can't change the direction of the
    wind, but I can adjust my sails to
    always reach my destination."
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