[FieldTrip] gradiometer definitions after ft_megplanar

Eelke Spaak eelke.spaak at donders.ru.nl
Mon Dec 9 09:19:04 CET 2013

PS: Note that a bug is assigned to me to facilitate ft_megplanar after
reprojection without artificially restoring the grad
(http://bugzilla.fcdonders.nl/show_bug.cgi?id=2332), so this should be
fixed at some point.

On 9 December 2013 09:16, Eelke Spaak <eelke.spaak at donders.ru.nl> wrote:
> Hi Ana,
> Are you by any chance doing ICA followed by ft_rejectcomponent at some
> point before ft_megplanar? After rejecting a component, grad.chanpos
> and grad.chanori will contain only NaNs (as of some months ago
> indeed), as the channel positions are ill-defined at that point (i.e.
> each 'data'-channel is in fact a weighted mixture of the original,
> physical, MEG channels). Since ft_megplanar needs the channel
> positions, it can no longer operate on data after ft_rejectcomponent.
> However, there is an easy workaround: the original channel positions
> should quite nicely approximate the positions after
> ft_rejectcomponent. So, what I do is simply store the original
> data.grad somewhere, and then make sure to stick in the data just
> before ft_megplanar.
> Note that the reason why ft_rejectcomponent updates the grad is that
> creating an accurate forward model (for source reconstruction)
> requires accurate sensor information. Therefore it fills grad.chanpos
> with NaNs, while updating grad.coilpos etc. to reflect the new
> projection. So you should *not* use the original grad for source
> analysis after ft_rejectcomponent, in that case just use the updated
> one with the NaNs inside.
> Best,
> Eelke
> On 8 December 2013 22:44, Todorovic, A. <a.todorovic at fcdonders.ru.nl> wrote:
>> Dear 'trippers,
>> I am attempting to do a TFR on planar gradient data. I first preprocess, then do ft_megplanar, then ft_freqanalysis, followed by ft_combineplanar. However, upon doing ft_megplanar, the grad.chanori field consists only of NaNs. I see that some changes were made a few months ago on how gradiometers are described, so I am wondering whether there are some changes I should now make to the cfg structure when doing the planar gradient transformation.
>> This is how I normally do it:
>>         cfg = [];
>>         cfg.planarmethod = 'sincos';
>>         cfg.channel = {'MEG'};
>>         cfg.trials = 'all';
>>         cfg.neighbours = neighbours; % neighbours=ft_prepare_neighbours(cfg,data)
>>         data_planar = ft_megplanar(cfg,data);
>> Alternatively, is there some workaround I could now implement to fix my already calculated TFR structures?
>> Cheers,
>> Ana
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

More information about the fieldtrip mailing list