[FieldTrip] channel order changes after ft_channelrepair

[Jörn M. Horschig]

Hi Fred,

yes, immediately after preprocessing it should be only those two fields. 

Best,
Jörn


--

Jörn M. Horschig, Software Engineer
Artinis Medical Systems  |  +31 481 350 980 

> -----Original Message-----
> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-
> bounces at science.ru.nl] On Behalf Of Frédéric Roux
> Sent: Tuesday, March 10, 2015 3:37 PM
> To: FieldTrip discussion list
> Subject: Re: [FieldTrip] channel order changes after ft_channelrepair
> 
> Dear Joern,
> 
> thanks for the quick and very helpful reply.
> 
> My goal is indeed to keep the channel order consistent across different
> participants.
> 
> After MF-preprocessing some of the channels are missing in certain
> participants but this is not consistent so I would like to interpolate the missing
> channels for those participants for which the channels were turned off.
> 
> I am guessing that the fields that I need to adjust if I want to manually re-
> order the info of the channels according to the template are
> 
> meg_data.label
> and
> meg_data.trial
> 
> Do you see anything else that would need to be adjusted ?
> 
> Best,
> Fred
> 
> --
> FR
> 
> ----- Original Message -----
> From: "Jörn M. Horschig" <jorn at artinis.com>
> To: "FieldTrip discussion list" <fieldtrip at science.ru.nl>
> Sent: Tuesday, March 10, 2015 3:16:30 PM
> Subject: Re: [FieldTrip] channel order changes after ft_channelrepair
> 
> Hi Fred,
> 
> back then when I implemented different options for channel interpolation,
> we decided that there is no "natural" order of channels in any sense. For
> MEG systems it might seem like that, because afaik there is a single
> acquisition software per system, which is always returning channels in the
> same order. However, this order is arbitrary and can be other rationales
> equally valid than the one used by the acquisition software.
> 
> For your specific case, I imagine that a sensor is broken and thus turned off: it
> will not be in the list of channels anymore. FieldTrip does not know where
> the 'natural' position of that channel is, as FT is not maintaining fixed channel
> lists. But this shouldn't be a problem anyhow, as channel labels can be easily
> matched. If I recall the latest developments correctly,  by now all FieldTrip
> functions are taking care of the channel order - even when computing
> leadfields ;)
> 
> If you do not like this due to aesthetical reasons or because you want to have
> the channel order being consistent across subjects, you can simply reorder
> them manually. As said, FieldTrip does not care about the order. Just be sure
> that if you are reordering the label-field, you also need to reorder the
> channel dimension(s) of all data.
> 
> If you encounter any problems with this concatenation, feel free send out
> notification.
> 
> Best,
> Jörn
> 
> PS: if the channel is already in your data and you want to just repair it
> because it suffers from a lot of artifacts, you could try using cfg.badchannel
> instead of cfg.missingchannel. If I recall correctly, missing channels are always
> concatenated, bad channels are kept in order if already present. But it's been
> a while, so I am not sure and right now, too lazy to check the code ;)
> 
> --
> 
> Jörn M. Horschig, Software Engineer
> Artinis Medical Systems  |  +31 481 350 980
> 
> > -----Original Message-----
> > From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-
> > bounces at science.ru.nl] On Behalf Of Frédéric Roux
> > Sent: Tuesday, March 10, 2015 3:05 PM
> > To: FieldTrip discussion list
> > Subject: [FieldTrip] channel order changes after ft_channelrepair
> >
> > Dear all,
> >
> > I just noted that after calling ft_channelrepair the order of channel
> > labels in my Neuromag 306 data has changed.
> >
> > The code I am using is as follows (fieldtrip-20150115):
> >
> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > % get the labels from the reference layout cfg = []; cfg.layout =
> > 'neuromag306planar.lay';
> >
> > [ref_lay] = ft_prepare_layout(cfg);
> >
> > % eliminate COMNT and SCALE labels
> > ref_lay.label = ref_lay.label(1:204);
> >
> > % get the labels of channels present in the data orig_label =
> > meg_data.label;
> >
> > % compare labels from reference layout with original data idx =
> > zeros(length(ref_lay.label),1); for it = 1:length(ref_lay.label)
> >    idx(it) = any(strcmp(ref_lay.label(it),orig_label));
> > end;
> >
> > % load the template neighbourhood structure from fieldtrip
> > load('neuromag306planar_neighb.mat');
> >
> > cfg = [];
> > cfg.neighbours = neighbours;
> > cfg.missingchannel = find(idx==0);
> > cfg.method = 'spline';
> >
> > [meg_data] = ft_channelrepair(cfg,meg_data);
> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >
> > When I then look at meg_data.label I can see that the missing channels
> > were added at the end of the channel label list instead of being
> > integrated in the list at the position where they would be found in
> > the channel list of the template layout.
> >
> > For instance
> >
> > meg_data.label(end) = 'MEG1133';
> >
> > and
> >
> > ref_lay.label(end) = 'MEG2643';
> >
> >
> > Does anyone know why this happens and how this can be avoided or
> > compensated? I am guessing that later on in the analysis pipeline this
> > can become problematic as the mapping between the new labels and the
> > spatial coordinates does not correspond anymore.
> >
> > Any help or suggestions would be highly appreciated!
> >
> > Thanks,
> > Fred
> >
> > --
> > Frédéric Roux
> > Postdoctoral Scientist
> > f.roux at bcbl.eu
> > Tel: +34 943 309 300 Ext 211
> > Fax: +34 943 309 052
> >
> > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
> > ----------------------------------------------------------------------
> > -----
> >
> >
> >
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> 
> 
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