megplanar input structure

[jan-mathijs schoffelen]

Dear Akiko,

I think that your crash may be related to the issue of missing
channels. Antony already pointed you to a way how to fix this. As to
your first question: ft_megplanar indeed works with data containing a
trial field (as cell-array). However, no need for you to worry about
this; if your input data is for example a 'timelock' structure,
fieldtrip automatically converts this structure into one containing a
'trial'.

Best wishes,

Jan-Mathijs


On Sep 20, 2010, at 11:54 PM, Akiko Ikkai wrote:

> Hello,
>
> I'm trying to calculate the planar gradient for my MEG data. I have
> 2 questions:
>
> 1. in tutorial "Event related averaging and planar gradient",
> (ft_)megplanar appears to call for averaged data created with
> cfg.keeptrials = 'no'; (how it was calculated earlier in the page),
> which looks like: (from tutorial)
>
> avgFIC =
>         avg: [149x900 double]
>         var: [149x900 double]
>     fsample: 300
>  numsamples: [77x1 double]
>        time: [1x900 double]
>         dof: [149x900 double]
>       label: {149x1 cell}
>      dimord: 'chan_time'
>        grad: [1x1 struct]
>         cfg: [1x1 struct]
>
> However, megplanar looks for data.trial (e.g. line 252). If I feed
> in averaged data with  cfg.keeptrials = 'yes'; input structure looks
> like: (from my data, after timelockanalysis with cfg.keeptrials =
> 'yes';)
>
> timelock =
>
>        avg: [156x751 double]
>        var: [156x751 double]
>    fsample: 500
>       time: [1x751 double]
>        dof: [156x751 double]
>      label: {1x156 cell}
>      trial: [72x156x751 double]
>     dimord: 'rpt_chan_time'
>        cfg: [1x1 struct]
>
> However, data.trial is matrix instead of cell structure, as
> megplanar requires (e.g. line 505:
> interp.trial{i} = transform * data.trial{i}(dataindx,:);  ), it
> crashes here.
>
> Also in tutorial, it appears that the sequence of analysis is
> ft_megplanar -> ft_timelockanalysis -> ft_combineplanar, where I
> suspect ft_timelockanalysis should be before calculating planar
> gradients...?
>
>
> 2. How to deal with bad channels in calculating planar gradient? It
> is suggested that we do preprocessing, timelockanalysis, megplanar
> and combineplanar. However, if I have bad channels and reject them
> in preprocessing, combineplanar crashes @ line 326
>
> if all(size(orig.pnt)==[302 3]) && ...
>    all(size(orig.pnt)==[302 3]) && ...
>    all(size(orig.tra)==[302 302]) && ...
>    length(orig.label)==302 && ...
>    all(sum(orig.tra~=0,1)>2)
>
> because length(orig.label) is not going to be 302. Could I simply
> change these lines to something like:
>
> if all(size(orig.pnt)==[length(orig.label) 3]) && ...
>    all(size(orig.pnt)==[length(orig.label) 3]) && ...
>    all(size(orig.tra)==[length(orig.label) length(orig.label)]) && ...
>    all(sum(orig.tra~=0,1)>2)
>
>
> If anyone could clarify these issues, I'd greatly appreciate it.
> Thanks in advance! Akiko
>
> ----------------------------------
> 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.