[FieldTrip] layout file error after upgrading to the newest version
Marta Topor
m.topor at surrey.ac.uk
Mon May 31 13:36:10 CEST 2021
Hi Jan,
Thank you so much for your insightful response. It all makes much more sense now - I apologise for my confusion with this.
My preference for sticking with the "spline" method was motivated by the fact that I had already processed over 40 files using the initially provided configurations and I wanted to keep my methodology consistent going forward with the project.
I can confirm that changing the method to average and replacing the cfg.elec configuration with cfg.layout ?works fine - which is great news!
Thanks again for your help and all the best!
_________________________
Marta Topor
PhD Candidate
Room 07AC04
School of Psychology
University of Surrey
________________________________
From: fieldtrip <fieldtrip-bounces at science.ru.nl> on behalf of Schoffelen, J.M. (Jan Mathijs) via fieldtrip <fieldtrip at science.ru.nl>
Sent: 28 May 2021 7:47 PM
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Cc: Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen at donders.ru.nl>
Subject: Re: [FieldTrip] layout file error after upgrading to the newest version
Hi Marta,
Rather than just trying out more or less all kinds of possible solutions, I suggest to step back and think about what you want to achieve:
You seem to want to call ft_channelrepair and use the ’spline’ method to interpolate between non-bad channels, to get a modelled signal for the bad channels.
So far so good.
Now, in order to use the ’spline’ method, you need to supply a geometric description of the channels, a.k.a. an elec structure, which is a matlab structure that at least should specify the 3D positions of the electrodes. This is different from a layout, because a layout is a 2D schematic of the channel array that can be used for topographical visualization. Also, it could be that another method in ft_channelrepair does not require a set of 3D channel position, but only requires a definition of channel neighbours (without position information). So, you either need to supply ft_channelrepair with 3D channel position information for the ’spline’ interpolation, or you should consider using a different interpolation method.
What you should know, is that the information in the layout structure, pertaining to the channel positions, is stored in the field <name-of-the-variable>.pos, whereas in an elec structure, the channel positions should be represented as <name-of-the-variable>.chanpos, so your attempt in adding a column of zeros is not only wrong in the sense that it would have led to a distorted spline interpolation, it is also not going to work due to a difference in fieldnames.
Long story short, if you require ft_channelrepair to use a method that needs a sensor description, you need to pass a valid sensor description in the cfg, OR in the data argument.
Please consult the documentation
https://www.fieldtriptoolbox.org/faq/how_are_electrodes_magnetometers_or_gradiometers_described/<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Ffaq%2Fhow_are_electrodes_magnetometers_or_gradiometers_described%2F&data=04%7C01%7Cm.topor%40surrey.ac.uk%7Cc8711cadd94f4882b00908d9220a2385%7C6b902693107440aa9e21d89446a2ebb5%7C0%7C0%7C637578249223142833%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=uHVfP656H6is07lxRBQfJEaMRPsPCGUWT95vEApE8hA%3D&reserved=0>
for a more detailed description of an elec-array.
Best wishes,
Jan-Mathijs
On 28 May 2021, at 15:59, Marta Topor via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:
Hi Tzvetan,
Thank you for your quick response, much appreciated!
I have spent a bit of time today trying to work this out.
If I do not include the cfg.elec line, I get another error:
Error using ft_fetch_sens (line 202)
no electrodes, gradiometers or optodes specified.
I have checked through my code and files thoroughly and I do not have a 3D layout file. I initially created my layout file from an image and it has always been in 2D. It seems that when I was running the code before, it worked OK with the 2D file.
Do you have any ideas for getting around this issue? I tried adding 0s throughout the layout structure to "pretend" it was 3D but it also did not work that way.
Thanks again and best wishes,
_________________________
Marta Topor
PhD Candidate
Room 07AC04
School of Psychology
University of Surrey
________________________________
From: fieldtrip <fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>> on behalf of Tzvetan Popov <tzvetan.popov at uni-konstanz.de<mailto:tzvetan.popov at uni-konstanz.de>>
Sent: 28 May 2021 7:37 AM
To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: Re: [FieldTrip] layout file error after upgrading to the newest version
Dear Marta,
In your cfg.elec, a 3D description of electrodes positions is expected. Yet you have a 2D layout structure. I assume that your neighbours are also defined in this 2D plane.
Can you comment out the cfg.elec line and try again? Ft_read_sens is not supposed to work on 2D layout file, hence the error.
Good luck,
tzvetan
On 27 May 2021, at 22:24, Marta Topor <m.topor at surrey.ac.uk<mailto:m.topor at surrey.ac.uk>> wrote:
Dear colleagues,
I came across a surprising error and I am struggling to figure it out.
I wrote a few scripts last year in version fieldtrip-20200409. They all worked fine, last time I worked with those scripts in that version was January 2021. I had to take care of a few other tasks since then, so the project was on pause. I had my work laptop upgraded in the meantime which meant I had to upgrade to the newest Fieldtrip version.
I started working on that same project again, in version fieldtrip-20210525, and noticed layout file issues when interpolating channels.
For a bit of background, I am using the Mobita water-based 32 EEG electrode system. I created my own layout file in the previous Fieldtrip version which worked without any issues in all scripts.
I now have an error using the ft_channelrepair() funtion and I think it relates to the ft_read_sens() funtion.
The cfg I used:
cfg = [];
cfg.method = 'spline';
cfg.neighbours = neighbours_EEG;
cfg.badchannel = badchannels_train;
cfg.senstype = 'EEG';
cfg.elec = layout_file;
mydata_interpolated_train = ft_channelrepair(cfg, mydata_artrm_train);
The layout file fields are:
pos: [34×2 double]
label: {34×1 cell}
width: [34×1 double]
height: [34×1 double]
outline: {1×4 cell}
mask: {[101×2 double]}
cfg: [1×1 struct]
But I can only see these fields if I use the function importdata(). When I use the function ft_read_sens() and when I try to interpolate channels, I get the following error:
Error message:
Unrecognized function or variable 'lab'.
Error in channelposition (line 352)
n = size(lab,2);
Error in ft_datatype_sens (line 438)
[chanpos, chanori, lab] = channelposition(sens);
Error in ft_datatype_sens (line 240)
sens = ft_datatype_sens(sens, new_argin{:});
Error in ft_datatype_sens (line 207)
sens = ft_datatype_sens(sens, new_argin{:});
Error in ft_datatype_sens (line 180)
sens = ft_datatype_sens(sens, new_argin{:});
Error in ft_read_sens (line 539)
sens = ft_datatype_sens(sens);
There are no errors when I plot the channels using the following code though and it all looks absolutely fine:
cfg = [];
cfg.layout = layout_m; %layout_m is imported from the layout_file using the importdata() function
cfg.channel = 'eeg';
ft_layoutplot(cfg, mydata_artrm_train);
Any ideas what could be the issue here and how I could get it solved?
Thanks for your help in advance!
_________________________
Marta Topor
PhD Candidate
Room 07AC04
School of Psychology
University of Surrey
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